Hydrologic changes in the mountainous regions would impact not only the physical watershed, but also the estuarine ecosystems. This is due to the fact that water quality in the San Francisco estuary is strongly driven by the volume and timing of freshwater inflows (4). Climate warming could also affect the aquatic species in the bay if salinity increases as previously mentioned (1). Only examples of fish species will be given here, although any alteration in estuarine habitat will ultimately affect all organisms living within.
Decreased freshwater runoff will increase estuarine water residence time in the spring and summer. The effects of altered residence times can be significant to some aquatic organisms. At their fastest growth rates, phytoplankton populations are able to double in number once or twice per day. If residence times increase as a result of altered freshwater delivery, phytoplankton will not be flushed out of the system, but will continue to double. This could create a eutrophic and possibly hypoxic situation as the phytoplankton populations use up the available oxygen in the estuary, which would then force out or kill the fish living in that region (10).
Shifts in the quantity, timing, and quality of freshwater flowing into the Bay is implicated in the declines of fish species and populations partly because of habitat changes resulting from altered flow patterns and salinity regimes (1). The reduced freshwater inflow and resulting increase in sality causes more salt-tolerant species to move upstream while freshwater species retreat (8). The problem for the freshwater species is that there is only so far to move before they lose essential habitat. In addition to this problem, fisheries managers are concerned that lower freshwater flows and higher water temperatures may disrupt spawning and larval transport (13).
There are about 130 regularly occurring fish species in the estuary (7, 2). Surprisingly, only two of these are strict estuarine fish (Delta smelt and Longfin smelt). The habitat necessary to support these estuarine fish could be lost as the salinity in the estuary increases. A quarter of the total fish species are freshwater fish, two-thirds are marine fish that range into the Estuary, and the remainder are anadromous fish. The locations and abundances of many of these fish species shift dramatically with changes in inflowing freshwater (7).
