Peregrine Falcons (Falco peregrinus) are adapting to urban settings around the world.  How urban settings compare to rural conditions at nest sites in a region has not been investigated.  We compared eight Peregrine Falcon nest site parameters at 25 urban and 20 rural nests in the San Francisco Bay Area, California, a region with diverse nesting opportunities and an abundance of prey, including waterbirds.  We suspected that conditions at urban sites would diverge from rural ones, exposing urban Peregrines to increased threats.  Using GIS and statistical comparisons, we found urban and rural nests did not differ with respect to some parameters, including solar radiation, wind speed, or distances to water.  But, urban nests experienced less precipitation, which may positively affect reproductive success, and were much closer to populations of two rare waterbird species.  Comparable distances to water indicate that Peregrines at urban and rural nests have similar access to waterbirds which may increase exposure risk to diseases such as Highly Pathogenic Avian Influenza.  In addition, the proximity to rare waterbirds brings Peregrines into direct conflict with management of those species.  Managers may use these findings to help develop multi-species plans that can maintain Peregrine Falcons and recover rare prey species.