It is paradoxical that San Francisco Bay (SFB), the largest estuary on the West Coast of the Americas and an iconic ecosystem for biological invasions, is understudied regarding quantitative data on free-living species, and virtually unexamined regarding their parasites.

I incorporate archaeological records, historical, and recent data to reconstruct the Bay's intertidal macroinvertebrate and shallow water fish assemblage circa 1850 AD to reveal a general shift in fauna from marine native to euryhaline exotic intertidal invertebrates. My findings suggest that the combination of biotic and abiotic forcing events impacted native species, especially mollusks and, with a time lag, resulted in the extirpation of many native species.

My assessment of the distribution and abundance of the native and exotic intertidal and shallow water fauna of SFB finds that the ratio of exotic to native species varies among habitat assemblages, Bay regions, and taxa. The majority of motile species are native, whereas the majority of sedentary/sessile species are exotic, and the densities of some native taxa are so low that they are at risk of extirpation.

Finally, I examine the Enemy Release Hypothesis in relation to metazoan parasitism and biological invasions. Community studies compare species richness, prevalence, and intensity of parasitism in similar natives and exotics within SFB. Biogeographical studies compare these metrics in SFB with populations of 5 exotic species in their native ranges, and with populations of 3 native species in other California estuaries. Exotic species in SFB experience enemy escape, but not always enemy release relative to similar native species. SFB populations of native species also experience partial release from digenetic trematodes relative to conspecifics in other estuaries.

Multiple invasions in SFB may have altered host-parasite relationships through reduced encounter among co-evolved, and increased encounter among novel, hosts and parasites. Collectively, in SFB it appears that most native trematodes using fish as second intermediate hosts will be able to complete their life cycles using exotic species, but that trematodes using invertebrates a second intermediate hosts, except for those that use the snail C. californica, may be unable to complete their life cycles, representing an invisible form of biodiversity loss.