Indeed, the extent of changes in the delta (e.g., Lund et al. 2010; see discussion of changing delta environments below) compound the effects of the many dams on major delta tributaries that remove habitat for migratory species whose passage is blocked by the dams (e.g., NMFS 2009).

Habitat is the physical and biological setting in which organisms live and in which other components of the environment are encountered (Krebs 1985, NRC 1995). Thus, all aspects of the delta, past and present, serve as habitat and all the environmental changes described in Chapters 1 and 3 affect habitat and the species that depend on it. Many efforts have been made and are ongoing to measure and assess habitats in terms of their suitability for organisms (e.g., NRC 2008a). The habitats of the delta are diverse in character and include the water column; submerged substrates; adjacent intertidal, wetland, and upland areas; agricultural fields; levees; rivers and streams; the estuary; and so on. All of them have changed markedly in the past 150 years. Based on the complexity of delta habitats and the modifications to them, the interactions between stressors (for example, the interactions among temperature, salinity, and invasive cyanobacteria) must be considered.

In many cases, substantial knowledge exists around habitat needs for individual species. For example, much is known about what salmon need with respect to temperature, water flows and velocities, turbidity, water depths, substrate and gravel types, seasonality of many of the preceding factors, riparian vegetation, and especially access (e.g., see Williams 2006, McLain and Castillo 2010, NMFS 2009). For delta smelt, important habitat factors include open water, semienclosed bays, flow rates and volumes, temperature, turbidity, and salinity. The list of factors increases when habitat for their prey is also considered. Changes in pelagic fish habitat have been described (e.g., Nobriga et al. 2008). One key aspect for pelagic organisms is that, unlike species that require specific substrate conditions, high-quaity habitat (and, similarly, low-quality habitat) for these species shifts location with changes in water conditions, especially in tidal areas. Thus, management of the salinity gradient, for example, in the estuary has important implications for delta smelt and other pelagic species.

The delta ecosystem will never return to its predisturbance state. Changes in the template combined with changes in community composition provide a context for efforts to “restore” the delta. The changes in delta geometry in the past 150 years, in both vertical and horizontal planes, have resulted in a system dominated by subsided islands and deep, levee-bound channels. The continued loss of peat from the islands combined with rising sea level continues to lead the system away from its former topography and bathymetry (Mount and Twiss 2005). Recent studies (Brooks et al. 2012) point to subsidence of 3 to 20 mm per year associated with compaction of underlying Quaternary sediments. Brooks et al. conclude that “[b]y 2100,

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