Extreme climatic events such as drought, floods, and heat waves are increasing in frequency and severity due to climate change, leaving estuarine communities susceptible to significant ecological consequences. Extreme rainfall causes low salinity in parts of San Francisco Bay, and as a result native Olympia oysters (Ostrea lurida) have experienced multiple mass mortality events over the past decade. Existing studies have evaluated the short-term impacts of these events on survival and recruitment, but not decadal-scale population trends. Olympia oyster population density and recruitment in San Francisco Bay were monitored from approximately 2009 to 2022 to identify spatial refuges which could support population stability in the face of low salinity and high temperature events intensified by climate change. I found that oyster density and recruitment generally increase with distance upstream in the estuary. However, the populations with the highest average density and recruitment endure far more exposure to episodic high temperature and extreme freshwater outflow events, and therefore experience enormous booms and busts over time. Compared with sites near the mouth of San Francisco Bay, the farthest upstream site experienced approximately 4 times more exposure both to high temperatures (≥30°C) across the study period and to low salinity (≤5 psu) in a record-breaking wet year. This difference was even greater when compared with the downstream region of San Francisco Bay. Results indicate that upstream sites are already experiencing more extreme conditions than other regions of the estuary, and such exposure will likely become more frequent and severe with climate change. These findings highlight the benefits of a multi-site conservation approach for Olympia oysters that prioritizes sites in the central region of San Francisco Bay for the best balance between protection and strong population metrics, while conserving upstream sites for their high density and recruitment during dry years, and downstream sites for the greatest protection from climate extremes. Understanding the spatiotemporal impacts of extreme climatic events is a key step in advancing climate change-resilient estuarine conservation.