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Summary The St. Johns River is the longest river in Florida, flowing 310 miles from Indian River County north to the Atlantic Ocean. The river drops only 30 feet from its headwaters to its mouth, such that the river has extensive freshwater wetlands, numerous large lakes, a wide estuarine channel, and a correspondingly diverse array of native flora and fauna. Water resource management in the river’s watershed, which accounts for 23 percent of Florida’s land area, is the responsibility of the St. Johns River Water Management District (the District). The District must provide water for the region’s 4.4 million residents as well as numerous industrial and agricultural users, all while protecting natural systems within the river basin. With population growth in the watershed expected to surpass 7.2 million in 2030, the District, through its water resources planning process, has begun to identify alternative sources of water beyond its traditional groundwater sources. Water reuse, desalination, and new surface water supplies are all under consideration, including the potential withdrawal of 262 million gallons per day (MGD) from the St. Johns River. To more comprehensively evaluate the environmental impacts of withdrawing this water from the river, in early 2008 the District embarked on a two-year Water Supply Impact Study (WSIS). Later that year, the District requested the involvement of the National Research Council (NRC) to review scientific aspects of the study and provide advice to its ongoing effort (see Chapter 1 for the NRC committee’s statement of task). This first report of the committee reviews the Phase I work of the WSIS and provides recommendations for improving Phase II. The report is organized along the lines of the seven scientific workgroups of the District, which include hydrologic and hydrodynamic modeling, biogeochemistry, plankton and water quality, benthos, the littoral zone, fish, and wetlands and wetland-dependent species. It should be noted that the WSIS does not consider the largest tributary to the St. Johns, the Ocklawaha River, to the same degree as the St. Johns River itself because (1) the Ocklawaha is hydrologically distinct from the St. Johns, (2) a focused study on the St. Johns River was more feasible given time and resource constraints, and (3) a separate analysis of minimum flow and level requirements for the Ocklawaha River is planned for the near future. Additionally, the WSIS does not consider the impacts of population growth that an additional water withdrawal of 262 MGD could support, as the District has no direct authority over growth and associated land use changes in the basin. OVERARCHING ISSUES In its assessment of the WSIS, the committee found that several issues transcended the discipline-based topics of the individual workgroups. Three are discussed here, with additional issues found in Chapter 2. The committee feels that these should be the highest priority issues 1

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2 Review of the St. Johns River Water Supply Impact Study: Report 1 for the District to consider as Phase II commences. Directing resources towards these issues now (as opposed to some of the individual projects felt to be of less importance—see Chapter 4 for details) would be in the best interests of the District in order to fully understand the effects of the proposed water withdrawals. Integration There is a substantial need for integration among workgroups as the WSIS proceeds, such that the output from one workgroup serves as input to another group for an iterative analysis of ecosystem impacts. Although results from the hydrodynamic and hydrologic modeling are being readily incorporated into the plans of the other workgroups, it is not clear that information exchange goes in the opposite direction or that the ecological workgroups are sufficiently linked to one another. For example, changes in the benthic macroinvertebrate assemblage may engender changes in the fish assemblage. Oral discussions with the District indicate recognition of this issue, but the Phase I report does not provide much evidence for integrative and cross- workgroup analyses. One way of facilitating integration of the seven workgroups would be for the District to develop a conceptual framework of qualitative interactions that link various ecological and physical parameters affected by surface water withdrawals. Not only would such a framework be an important communication tool for the District, but it could also be used to better connect the field studies, models, and analyses that are part of the WSIS. Along with this framework, the District might provide a clearer set of testable hypotheses and quantitative research questions that link the hydrodynamics and hydrology of the WSIS to the ecology and reflect the state of knowledge along with the planned studies. That is, the proposed conceptual framework described above provides organizing principles for qualitative understanding of the linkages, whereas the hypotheses and research questions provide the guidelines for the scientific efforts required to quantify the linkages. Finally, several workgroups of the WSIS are analyzing the potential impacts of additional water withdrawals on individual indicator species of submersed aquatic vegetation (SAV), benthos, fish, and birds—an approach that could hinder the ability of the District to achieve integration. It generally is not clear whether the most sensitive species are being considered. Moreover, reliance on single species as indicators of change may underestimate community-level impacts and may ultimately limit the District’s ability to understand a variety of important ecological dynamics caused by water withdrawals. Water and Nutrient Budgets and Return Flows It will be important for the District to assemble basic water and nutrient budget information for the St. Johns River basin and its major subunits. These budgets should include the standard sources, sinks, and storage components of such budgets, as well as information on how these components vary over time. The purpose of such budgets is primarily to better understand the proposed water withdrawals relative to current conditions in the St. Johns River. The District estimates that the proposed continuous withdrawal at DeLand, Florida, would

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Summary 3 constitute approximately 7.8 percent of the average daily flow over the period of record. This is a significant fraction that would increase under low flow conditions. Nutrient budgets are needed to conduct a credible analysis of the impacts of water withdrawals on algal blooms in the river and especially in the large lakes that constitute major parts of middle portion of the St. Johns River. Comprehensive information on nitrogen and phosphorus loadings to the system currently is lacking or at least has not been assembled in a system-wide way. Finally, potential water withdrawals are treated in the WSIS as consumptive uses with no return flows of withdrawn water to the system—a conservative assumption according to the District. Although it is difficult to estimate future patterns of consumptive water use, given uncertainties regarding future climatic and land-use conditions, data are available on past and current consumptive and non-consumptive uses of water in the drainage basin for the District to be able to provide a range of scenarios of the extent to which future withdrawals will be consumptive. Dewatering of Floodplains and Wetlands The Phase I hydrodynamic and hydrologic modeling studies suggest that the decline in surface water levels produced by the proposed water withdrawal will be small, from 1 cm to at most 4 cm. This result has played a role in guiding the Phase I work of the biogeochemistry, SAV, benthos, fish, and wetlands workgroups. Although initial consideration of this result might suggest that the likely environmental effects of water withdrawal will be minimal, the District should avoid a rush to judgment. First, more careful analysis in the form of advanced hydrologic and wetland modeling is needed to determine the area to be dewatered as a result of lower water levels, including the timing and duration of dewatering events. This type of modeling will be a part of the Phase II studies of the hydrodynamics and hydrologic and wetlands workgroups. In addition, an effort should be made during Phase II to determine the nature and areal extent of locations that may experience altered biology due to partial dewatering of wetlands and floodplains. Indeed, gaining more definitive information on the areal extent of dewatering would be more immediately valuable to understanding the environmental impacts of water withdrawal than several of the literature and monitoring studies suggested for Phase II (see Chapter 4 for details). HYDRODYNAMIC AND HYDROLOGICAL MODELING Extensive surface water and groundwater modeling was conducted as part of Phase I of the WSIS. The surface water hydrodynamic and hydrological studies focused on understanding the changes in surface water depth, discharge, water age, salinity, turbidity, and wetland dewatering caused by surface water withdrawals from the St. Johns River. The Phase I studies were screening studies based on readily available historical data and hydrological models. The workgroup developed hydrodynamic models of the lower and middle St. Johns River, it evaluated salinity under different scenarios for the lower river, and it conducted a model analysis of possible changes in sediment loading in the middle river. They concluded that water stage in the lower and middle river will be relatively unchanged by surface water withdrawals. Channel

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4 Review of the St. Johns River Water Supply Impact Study: Report 1 dredging and surface water withdrawals were predicted to increase salinity in the lower St. Johns River more than rising sea level and wastewater diversion. However, the analysis focused on increases in average salinity and did not discuss extremes. It will be important for the Phase II modeling and analyses to be tied carefully to the time–space scales of salinity that are important to ecology; indeed, the hydrodynamic modelers should have a documented process for determining scenarios and data needs for the other six workgroups. Overall, the District is progressing along the correct track with respect to the surface water studies, but critical details either have not been considered or have not been sufficiently documented. Specifically, the District should work to connect the separate modeling and analysis efforts of Phase I. For example, the Phase I analyses did not examine how hydrologic changes in specific river sections relate to changes or effects in the rest of the river. Second, several areas were not studied or explained in enough detail during Phase I, including modeling of extreme conditions, the hydrology of the upper St. John River, vertical gradients of salinity and horizontal upstream salinity excursions in the lower river, and the effects of bridges and sea level rise. Third, the District should document model calibration and sensitivity and develop methods to quantify model uncertainty on the time–space scales at which ecological effects occur. The primary goal of the Phase I groundwater modeling was to predict whether discharges of groundwater into the St. Johns River would change if the river stage dropped due to water withdrawals. Two groundwater flow models were used during Phase I to compute groundwater base flows along the river from the surficial aquifer system and the upper Floridan aquifer: the North Central Florida and the East Central Florida MODFLOW models. The groundwater analyses were confined to the middle and upper St. Johns River basins. Based on the modeling results, the change in the average discharge of groundwater following water withdrawal was not predicted to be particularly significant in the middle and upper basins, although the change in chloride flux was predicted to be significant. This conclusion may be correct, but it is not yet technically defensible due to limitations in the models. In order to improve the groundwater modeling in Phase II of the WSIS, the District should consider using a transient model that includes wetlands processes (e.g., the East-Central Florida Transient [ECFT] model) and a cross-sectional density-dependent model. ECFT would be a valuable screening tool to better understand how groundwater flow into the river will vary with water withdrawals due to its representation of various seasonal changes, wetland simulation capabilities, and increase in horizontal resolution. A two-dimensional, cross-sectional, density- dependent model could be developed to indicate the vulnerability of certain river segments to changes in saline flow from groundwater following potential water withdrawals from the river or other alternative water management scenarios. This would be most valuable in regions of the river known to be susceptible to saltwater intrusion. ECOLOGICAL WORKGROUPS In the Phase I study, six workgroups used hydrologic modeling data, existing monitoring data, and literature reviews to provide preliminary assessments of potential biogeochemical and ecological impacts in the St. Johns River from withdrawing 262 MGD of surface water. Chapter 4 provides assessments of the Phase I work on biogeochemistry; plankton, nutrients, and total maximum daily loads (TMDLs); the littoral zone; benthos; fish; and wetlands and wetland- dependent species. This summary includes only a subset of the concerns held by the committee

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Summary 5 with regard to each workgroup. Additional detail can be found in the individual sections of Chapter 4. Biogeochemistry The biogeochemistry workgroup identified seven potential effects of additional water withdrawals on biogeochemical processes, all related to the possibility that soil accretion will be reduced and/or oxidation of organic soils will be enhanced in the extensive floodplains of the St. Johns River as a consequence of changes in river stage induced by additional water withdrawals. The Phase I study involved calculations based on literature values for release rates of various constituents from flooded and exposed organic soils. None of the literature values of substance release rates used in the Phase I study appears to be from soils in the St. Johns River Basin. Three of the potential effects were considered to have potentially high significance: (1) reduced nutrient sequestration, (2) increased release of colored dissolved organic matter (CDOM), and (3) increased production and reduced sequestration of greenhouse gases produced within inundated organic soils. Preliminary results were presented for inorganic phosphorus release only, although the work plan for Phase II indicates that nitrogen will be addressed by undertaking appropriate data collection. The Phase I report did not make a persuasive case that changes in CDOM concentrations or loadings under conditions of additional water withdrawals would have significant ecological or water-quality impacts. If laboratory experiments are undertaken during Phase II to obtain local nutrient and CDOM release rates from drained soils, the workgroup should use procedures that will yield data reflective of environmental conditions. It is critically important that sufficient samples be analyzed to address the well-known large heterogeneity found in soils. Experimental studies should be done at as large a spatial scale as possible to avoid artifacts caused by trying to extrapolate results from small sample sizes and small containers to the ambient environment. Finally, it may be premature to conduct extensive laboratory and field experiments to evaluate rates of nutrient and CDOM release from drying soils of riparian wetlands in the St. Johns River Basin. A sequential approach would be more effective, in which additional analyses establish the areal extent of wetland soils that would be dried to a sufficient extent and for a sufficient duration to enhance oxidation of soil organic matter and subsequent release of nutrients and CDOM. If these studies indicate a high likelihood of effect, then experimental studies (at mesocosm rather than microcosm scales) could be undertaken to measure rates of nutrient and CDOM release under environmental conditions relevant to the proposed water withdrawal scenarios. Plankton, Nutrients, and TMDLs The plankton and TMDL workgroup was tasked with identifying and quantifying possible environmental impacts of water withdrawals on plankton communities and existing TMDLs in the lower and middle St. Johns River. Overall, the workgroup did a commendable job summarizing and interpreting archival data from a variety of studies conducted in the middle and lower reaches of the St. Johns River over the past 25 years. However, several critical issues were not considered.

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6 Review of the St. Johns River Water Supply Impact Study: Report 1 First, additional water withdrawals may increase the likelihood, duration, and areal extent of water column stratification and bottom water hypoxia in the lower St. Johns River under low- flow conditions, which was not discussed in the Phase I report. Second, the Phase I report does not adequately address the type or frequency of additional water quality and biological monitoring data needed to adequately assess the impacts of water withdrawals on TMDLs and plankton. Phase II plans include monitoring only in Lake George. Third, it appears that the District has concluded that phosphorus is the limiting nutrient for algal growth in the freshwater portions of the St. Johns River. The occurrence of substantial blooms of nitrogen-fixing cyanobacteria in Lake George is strong evidence that nitrogen limitation occurs at least at some times of year and in some locations within the river. A key goal for this workgroup during Phase II is to better estimate nutrient and CDOM loading for segments of the middle and lower St. Johns River under the various water withdrawal scenarios and how this will affect plankton dynamics. This will require tighter integration with the hydrodynamics and hydrologic and the biogeochemistry workgroups. The effects of high concentrations of CDOM (that may result from water withdrawals) on phytoplankton ecophysiology were not explored during Phase I, although the biogeochemistry workgroup did consider increased concentrations of CDOM. If further analysis from the biogeochemistry workgroup provides support for an effect of CDOM, then the plankton workgroup will need to consider how this may affect plankton growth in the river. Phase II work plans for the plankton workgroup indicate the District’s understanding of the importance of both nitrogen and phosphorus to plankton dynamics. Plots of nitrogen:phosphorus ratios as a function of potential controlling variables, such as discharge rates, residence time, and water age, could be useful for assessing potential impacts, especially as related to nitrogen-fixing cyanobacterial blooms. Finally, the workgroup is encouraged to continue the development and validation of three-dimensional water quality simulation models (e.g., CE-QUAL-ICM) for the major reaches and lakes of the St. Johns River. Benthos The benthos workgroup of the WSIS is studying benthic macroinvertebrates in both freshwater and brackish water environments to better understand the ecological consequences of water withdrawals in the St. Johns River. In the Phase I report, the workgroup reviewed past work in the watershed including an analysis of an existing data base, and it briefly described several conceptual models to guide thinking about how to study and understand the effects of water withdrawal on the trophic organization of benthic invertebrates. In addition to a focus on trophic organization, the Phase I report also targets a few invertebrates (e.g., crayfish, apple snail, blue crab, penaeid shrimp) as taxa of special interest that could be used as species-level indicators in the WSIS. Although the literature review evident from the Phase I report was extensive, it was not clear what lessons the workgroup would be applying to the St. Johns situation. For example, it was not clear which papers documented how invertebrate assemblages changed as a result of water withdrawal. Another subject not touched in the Phase I report is the effect of water withdrawal on macroinvertebrates with meroplanktonic larval stages, a group of taxa with high relevance in a comprehensive ecological assessment. This subject might be addressed jointly with the plankton workgroup during Phase II.

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Summary 7 The need to collect more data was recognized in Phase I, and a first-level plan was fleshed out in the Phase II work plan. In contrast to freshwater areas, the Phase II work plan concludes that no new data will be collected in the estuarine segments of the watershed. Instead, data from existing studies will be analyzed further with the goal of evaluating the effect of salinity and other water-quality variables on invertebrate community structure. Without more information on the context of those historical data collections (e.g., timing, spatial distribution, duration, kinds of data, data collection protocols), it is impossible to judge the merit of that decision. Rather, it would be better to defer any decision about additional data collection from the estuary until a careful evaluation of the utility of existing data is completed. Other factors— such as new dredging by the port authority or the U.S. Navy—that might affect salinity, sedimentation, or other conditions in the lower river may also require reevaluation of estuarine monitoring decisions. Overall, the committee supports the District’s commitment to study the effects of water withdrawal on benthic invertebrate communities. Unfortunately, the available data are insufficient to define precisely what the effects of water withdrawals on the benthos of the St. Johns River will be. The District is commended for sketching the rudiments of a sampling and data analysis program for Phase II, although much of the detail of those efforts is yet to be defined. Littoral Zone SAV is a focus of the WSIS because the proposed surface water withdrawals are likely to exacerbate salinity intrusions in the estuarine portion of the river, which could have detrimental effects on local SAV populations. The littoral zone workgroup is assessing the potential damage to SAV from the proposed water supply withdrawals via an extensive monitoring program. By assessing the condition of the SAV during high-salinity pulses in the lower river and comparing these data to literature values on salinity tolerance, the workgroup has made preliminary estimates of the effects of water supply withdrawals on SAV. The focus of the Phase I effort was the lower 131 km of the St. Johns estuary, where SAV abundance has been monitored intensively over the last 10 years. Most of the cover is due to Vallisneria americana, a perennial species with well-developed underground roots and rhizomes that are ideal for consolidating bottom sediments, providing oxygen to benthos and promoting nitrification. In addition, V. americana beds are excellent habitats for small fish. During Phase I, the District predicted that projected future water withdrawals could have dramatic consequences on SAV in some areas, especially where V. americana populations now fluctuate in the lower St. Johns River. Although V. americana presumably could migrate further upstream, there is less shallow water area there, so a net loss of habitat is still expected. Improved hydrodynamic and hydrologic modeling during Phase II is expected to provide more spatially explicit predictions of the salinity increases in the littoral zone. To enhance their monitoring program, the District should consider adding at least one continuous salinity monitoring station in the littoral zone during Phase II to detect short-term salinity excursions where V. americana is at risk. The workgroup should also undertake more study of salinity tolerance of local populations from the St. Johns River, perhaps via mesocosm studies, in order to validate the values derived from the literature. Finally, the workgroup might assess whether any other existing SAV species, for example Ruppia maritima, might be able to take the place of

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8 Review of the St. Johns River Water Supply Impact Study: Report 1 V. americana as a dominant macrophyte in the littoral zone. A mesocosm program similar to the one described above for V. americana would be helpful in this regard, although it is acknowledged that such experiments go beyond the planned Phase II work. Fish The District’s Phase I report describes how water withdrawals could influence spawning success and recruitment of important recreational and commercial fishes, populations and distribution of other fish species, and critical dimensions of fish habitat. Two potential effects were considered by the fish workgroup: (1) the direct effects from entrainment or impingement and (2) indirect effects associated with changes in habitat caused by water withdrawals. The District’s hypothesis is that given the relatively low intake velocities of the proposed water withdrawals, adult and juvenile fish entrainment or impingement probably will not be significant enough to elicit broad-based community changes. However, given the lack of information on entrainment and impingement of larval stages, the District has begun a study of larval fishes in five regional locations in the upper and middle basins of the river. It will be important for the District to clearly define the actual distribution and frequency of Phase II sampling, as this was not evident in the Phase I report or the Phase II work plans. The committee’s concerns include the frequency of larval fish sampling in these areas, the lack of nocturnal sampling, and the narrow focus on clupeid larvae. The Phase I report describes other potential environmental impacts to fishes as a result of water withdrawal, which can be much more difficult to assess. With respect to salinity effects, the District had contracted with the Florida Fish and Wildlife Conservation Commission to examine the influences of water level and salinity changes on fish in the lower river. Although this is a step in the right direction, there are significant limitations to this monitoring that need to be kept in mind. For example, this program does not collect samples in small creeks in the lower river and thus will miss important nursery areas. Finally, the fish data analyses need to be integrated with other components of the regional biota (e.g., benthos, decapods, SAV) that also may be influenced by salinity shifts. One last concern with the Phase I report is the lack of consideration of how water level decreases will influence fish population dynamics and distribution. The District should carefully study potential impacts to all fishes in the middle and upper St. John River but particularly those that require shallow areas for spawning and foraging, including but not limited to the centrarchids. The Phase II work plan makes progress in explaining the District’s approach to examining how water level changes might impact floodplain habitat for fishes. Wetlands and Wetland-Dependent Species Changes in hydrology can alter the structure and function of wetlands. Therefore, the wetlands workgroup is examining the potential impacts of the proposed surface water withdrawals to wetland vegetation communities and a few species of wetland-dependent fauna. Impacts range from changes in vegetation community type or structure (including species composition) and altered productivity to shifts in the position of boundaries between communities. The Phase I wetlands work was descriptive and conceptual in nature.

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Summary 9 A major concern of the committee is how the workgroup identified and delineated wetlands that are influenced by the river’s hydrology. The floodplain was delineated using the 5- foot contour line, with the assumption that the 5-foot elevation captures much of the 50-year floodplain. Unfortunately, this crude approach lacks the resolution necessary to predict the ecological effects of hydrologic change. Fine-scale elevation data in the form of a digital elevation model are needed to produce accurate maps in flat, wetland-rich areas (particularly in efforts to characterize hydrology); map wetland diversity; and anticipate likely changes in these distributions as a result of water withdrawal. The District plans during Phase II to produce digital elevation models for the portions of the watershed where LIDAR data are available. The wetlands workgroup divided the river into nine segments deemed relatively homogeneous in terms of soils, vegetation, hydrology, water quality, and fauna. For each segment, qualitative information was provided on the relative likelihood of impacts from water withdrawals to wetlands. The criteria used to determine the likelihood of impacts are not provided in the report, making it virtually impossible to judge the results. Finally, the District should consider broadening the range of taxonomic groups used in monitoring wetland impacts. Many wetlands in the floodplain are not used as habitat by the four chosen avian species, a problem compounded if the bird populations occur in low densities. Amphibians, reptiles, invertebrates, and plants have proven to be valuable indicators of hydrologic impacts to wetlands in monitoring programs and might be considered as indicators in Phase II. The district has proposed investigating additional species in the Phase II work plans; however, there is no detail or methodology provided on how the different assemblages presented (e.g., reptiles, amphibians) might be used to indicate impacts.