Understanding the conditions that drive variation in recruitment of key estuarine species can be important for effective conservation and management of their populations. The Olympia oyster (Ostrea lurida) is native to the Pacific coast of North America and has been a target of conservation efforts, though relatively little information on larval recruitment exists across much of its range. This study examined the recruitment of Olympia oysters at biweekly to monthly intervals at four sites in northern San Francisco Bay from 2010 to 2015 (except 2013). Mean monthly temperatures warmed at all sites during the study, while winter (January–April) mean monthly salinity decreased significantly during a wet year (2011), but otherwise remained high as a result of a drought. A recurring peak in oyster recruitment was identified in mid-estuary, in conditions corresponding to a salinity range of 25–30 and >16 °C at the time of settlement (April–November). Higher average salinities and temperatures were positively correlated with greater peak recruitment. Interannual variation in the timing of favorable conditions for recruitment at each site appears to explain geographic and temporal variation in recruitment onset. Higher winter/spring salinities and warmer temperatures at the time of recruitment corresponded with earlier recruitment onset within individual sites. Across all sites, higher winter/spring salinities were also correlated with earlier onset and earlier peak recruitment. Lower winter salinities during 2011 also resulted in a downstream shift in the location of peak recruitment.