Wetland loss, salinity changes, and higher temperatures are all likely to affect finfish and shellfish in the coastal zone. The most vulnerable species are those that either reproduce in coastal wetlands, spend their entire lifetimes in an estuary, or both.
Coastal marshes are the primary nursery grounds for crab, shrimp, menhaden and several other important fish. Most of the reproduction occurs in the part of the wetlands that are within about 50-100 feet of the open water, because fish find it more difficult to access parts of the marsh farther from the open water. As sea level rises and inundates wetlands, the initial effect in some areas is to increase the amount of channels through the marsh, which increases the total area of marsh to which the fish have access. Hence, sea level rise initially tends to increase the production of these species. As sea level continues to rise, however, the loss of marsh accelerates; and eventually most or all of the wetlands in an area are replaced by open bodies of water. Thus, in the long run, an accelerated rise in sea level would decrease production of these species.
A number of marine species that are not important for commercial fishing are also vulnerable to the inundation and erosion of coastal habitat. The horseshoe crab lays its eggs on sandy estuarine beaches of Delaware Bay 
and other beaches in the mid-Atlantic; officials in that region are already concerned that this species is being threatened by loss of sandy beaches (see Coastal Zones). The horseshoe crab and the birds that rely on a plentiful supply of their eggs could be further endangered as rising sea level increases the erosion of these beaches, especially if shores are armored. In Hawaii, seals and turtles nest on small sandy islands and sand spits, which could be eroded by rising sea level.
Estuarine species also are vulnerable to other implications of climate change. Oyster predators such as MSX and oyster drill require salty water; hence the increased salinity from rising sea level or increased drought could lower oyster harvests, which have already decline by more than 90 percent in the last several decades in many estuaries. Warmer temperatures could leave estuaries too warm for some of the current inhabitants: In Apalachicola Bay (Florida), for example, a warming of 7°F could cause several species to flee the bay on hot days for the cooler waters of the Gulf of Mexico, making them more vulnerable to predators; secile species such as clams and oysters would not have this option. The lower dissolved oxygen content resulting from warmer water could also lead to fish kills in some estuaries (see Water Resources - Recreation).
The impact of climate change on estuarine fisheries will depend in large measure on how state and local governments manage their wetlands and beaches. Even though a net loss of wetlands is likely, the narrow strip of marsh necessary to provide nurseries for some fish species will be protected in Rhode Island and other states that retain wetland shores rather than replacing them with bulkheads as sea level rises. Similarly, the conscious effort to preserve estuarine beaches in Delaware Bay is more likely to protect horseshoe crabs and other species than the gradual elimination of beaches that is occurring along Chesapeake Bay and other estuaries.
In addition to the estuarine species, coastal fisheries include several species that primarily inhabit the ocean near the shore, some of which reproduce in estuaries. Bluefish, Tuna, Mackerel and other species that inhabit the continental shelf would probably be able to migrate to the north as ocean temperatures warm. Along the Gulf of Mexico, rock lobster and other species that are found in commercial quantities around the southern portions of Texas and Florida could migrate north to the cooler Gulf waters of Alabama, Mississippi, and the Florida Panhandle. However, the ability of Gulf fish to migrate north would be limited by the lower salinity in the northern Gulf, which some Gulf species are unable to tolerate, as well as the coast itself. Fishing in the Gulf could also be harmed if warmer temperatures exacerbate the anoxic conditions (i.e., seawater with too little oxygen) that often prevail along parts of the northern Gulf Coast. (Please refer to the Gulf of Mexico Hypoxia Assessment. )
Approximately 50% of ocean fish, including shrimp, menhaden, flounder, sea trout, croker and red drum spend most of their lives in the ocean, but spawn in estuaries. As climate warms, these fish might be able to migrate north, as long as an estuarine environment remains available. The loss of wetlands from rising sea level may substantially diminish the critical coastal habits of shrimp and other fish that rely on the marsh. Moreover, scientists are unsure whether these fish would be able to shift to more northern estuaries. Some species tend to automatically seek the estuary in which they were born; as the water warms they may therefore tend to return to the same estuary even if it was inhospitably warm, rather than seek cooler waters. On the Pacific Coast, the small number of estuaries would further increase the difficulty of finding a cooler estuary if, for example, global warming were to leave San Francisco Bay too warm for the oceangoing fish that spawn there.