Estuaries provide important habitat for many fish and wildlife and are among the most imperiled ecosystems on Earth. One of the many challenges facing estuaries is increasing salinity from factors like sea level rise and reduced freshwater inputs from droughts and human water use. In the San Francisco Bay Estuary salinity is a nascent threat with looming management challenges for species like the Northwestern pond turtle (Actinemys marmorata, WPT). While WPTs in some parts of their range show behavioral and physiological adaptations to increased salinity levels, it is unclear how resilient they will be to future elevated salinity levels. We studied the effects of salinity on the distribution and occurrence of WPTs in Suisun Marsh, which consists of a mosaic of tidal and managed brackish water wetlands with a natural salinity gradient. We analyzed occurrence data from visual encounter surveys using dynamic occupancy models to predict occupancy as a function of environmental covariates. WPTs were observed at 65.8% of sites on at least one occasion and salinity was the most important factor associated with turtle occupancy, which decreased with increasing salinity. By understanding the role that salinity plays in determining the distribution of WPTs, managers can aid future conservation efforts.