Background/Question/Methods The San Francisco Bay is the largest estuary on the West Coast of the United States, and is heavily invaded and urbanized. We studied the largest watershed draining into San Francisco Bay, Alameda Creek, which encompasses over 1554 km2 and a wide range of habitats from highly urbanized lowland reaches to relatively pristine headwater reaches. From 1992-1996, we sampled 70 sites throughout the watershed to characterize reach-scale fish assemblage and environmental variables. We then re-sampled all of these sites during the summer of 2009. Here we (1) characterize changes in the diversity, abundance, and distribution of native and nonnative fishes between these two sampling events and then use a landscape approach to (2) quantify changes in land use across this period and (3) elucidate the relationships between the fish assemblage data collected in 2009 and large-scale land use patterns. Results/Conclusions Between the early (1992-96) and late (2009) sampling events, we found no new native fish extirpations and few changes in the diversity, abundance, and distribution of native fishes. One significant change in the fish assemblage was the introduction of the western mosquitofish (Gambusia affinis). This tolerant species used for mosquito abatement has spread to nearly every region of the watershed, excluding the undisturbed headwater tributaries. During this same time period, there have been extensive land use modifications within the Alameda Creek watershed. These transitions were primarily from rural/grasslands to low-moderate development, and from low development to high development. Initial results indicate strong associations between distinct fish assemblages and local environmental variables, in addition to significant correlations between fish presence/absence and watershed land use patterns. For example, we find that nonnative species are highly correlated with high rates of impervious surface within a 2km buffered region of its drainage basin. We conclude with a discussion of factors possibly contributing to the stability and resilience of native fishes in Alameda Creek despite significant landscape changes and the invasion of mosquitofish.