Background/Question/Methods The San Francisco Bay (Bay) is the largest estuary on the West Coast of the United States, and considered one of the most heavily invaded systems in the world. There are approximately 70 streams that flow into the Bay, many of which are surrounded by highly urbanized landscapes. Although these systems are heavily invaded and impacted, there is little known about the effects on native fishes. From 1993-1999, Leidy et al. sampled 275 sites within 23 watersheds. Here we provide an overview of the current status of native fishes in the small streams and emphasize several environmental variables associated with native fish assemblages. Results/Conclusions Despite the compounding impacts of habitat modification, pollution, changes to the natural flow regime, and the introduction of nonnative fauna, there persists a relatively diverse native fish assemblage. Based on historical records, only two species are locally extinct, tidewater goby (Eucyclogobius newberryi) and coho salmon (Oncorhynchus kisutch), and only one is globally extinct, thicktail chub (Gila crassicauda). In total 77 fish species were observed, 33 of which are native. Fifty-four percent of native fishes were found in headwater streams above 125 m, thus indicating a preference for relatively undisturbed conditions of middle-headwater elevations. Additionally, eighteen percent of the native fish species found are euryhaline marine, including 15 saltwater dispersants species. We postulate that salinity tolerance has assisted in the persistence of native fish by allowing for migration and recolonization to neighboring streams while restricting the frequency of invasions by nonnative fishes. Our observations suggest that urbanization is a complex phenomenon and its effects on native fishes vary greatly depending on multiple, interacting factors that are not well understood. To better understand the observed patterns of native fishes in Bay streams we are developing a GIS framework to elucidate the relationship between large-scale land use patterns and other environmental variables.