Coastal macroalgae provide ecosystem functions and services supporting a diversity of organisms and are often associated with increased species diversity and abundance. Fucus distichus is a habitat-forming macroalga that can dominate hard intertidal surfaces in estuarine environments.However, there are very few studies on the ecology of F. distichus in Northeastern Pacific estuaries. A variety of climate change stressors (increasing and more variable temperature and precipitation, increasing acidification of ocean and coastal waters, sea level rise), human development, and natural variability make urban estuaries a good model to examine dynamic systems and model future conditions. I addressed the following research questions using a combination of field and laboratory observations, statistical modeling, and a mesocosm experiment: 1) What is the distribution of F. distichus in the San Francisco Estuary (SFE)? 2) Do F. distichus populations vary over time? 3) Are variations in salinity, pH, or air temperature associated with changes in juvenile F. distichus abundance? 4) What is the reproductive phenology of F. distichus? And 5) How do salinity and pH influence the reproductive output of F. distichus? F. distichus was found throughout the San Francisco Bay (SFB) (San Pablo Bay, Central Bay, and South Bay) but was observed more frequently in the Central Bay and was not observed in the Delta. I studied four populations of F. distichus in the Central Bay of the SFE in more detail (Paradise Cay, Point Chauncey, Brickyard Park, and Horseshoe Bay) to improve our understanding of its abundance and reproductive ecology in a highly dynamic estuarine ecosystem. Although the overall patterns of salinity, pH, dissolved oxygen, water temperature, and air temperature were similar across sites, the maximum values, minimum values, and ranges varied among sites, with some differences among major events as well. F. distichus cover, total density, juvenile density, and adult density all generally decreased between June 2018 and September 2019. Cover tended to be less variable and stayed high even when total density was depressed between November 2018 and May 2019. However, juvenile densities began to recover between July and September of 2019.Overall Horseshoe Bay, the site closest to the ocean, had lower but more stable cover, total densities, and juvenile densities than the other sites. Environmental models of monthly juvenile density suggested that high variability in median daily salinity and pH range (or the number of low salinity (< 10) and high pH (>8) events), and high air temperatures (>26 °C) during low tide, all had negative effects. Density of adults had a positive effect, but only when air temperatures were high (>26 °C). Models including all these explanatory factors (versus only some of them) were the best (had the most information, lowest AICc) among the models examined. I did not find any evidence for a temporal trend or cycle in reproductive effort over time. Reproductive tissue and oogonia were found throughout the...