San Francisco Bay is the defining landscape feature of the place we call ‘The Bay Area,’ but most of us only experience the Bay as we view it from an airplane window or drive across one of its bridges. These views from afar suggest that the Bay is static and sterile, but this impression is deceptive. If you are one of the many thousands of students who have experienced the Bay through a school excursion with the Marine Science Institute or other educational programs, you observed its rich plankton soup under a microscope, sorted clams and worms and crustaceans from mud samples, and identified the gobies, sole, halibut, bat rays, sharks, sardines, and smelt caught with trawls. San Francisco Bay is much more than a landscape feature. It is a dynamic ecosystem, continually changing and teeming with life. The Bay once supported the most valuable fisheries on the west coast of the United States, but commercial fishing for shellfish, shrimp, sturgeon, shad, salmon, and striped bass ended many decades ago because of habitat loss, pollution, invasive species and over harvest.

Bay Area residents feel a sense of responsibility to protect San Francisco Bay and keep it healthy. Some even dream about the recovery of fish stocks so they can sustain commercial fishing once again inside the Bay. How is our Bay doing? Is it highly polluted or pretty clean? How does its health compare with other estuaries in the United States? Are things getting better or worse? Does costly wastewater treatment have benefits? What are the biggest threats to the Bay and how can we reduce or eliminate those threats? How will the Bay change in the future? These questions can only be answered with investments in study and monitoring, and they are the driving force behind the Regional Monitoring Program (RMP). We describe here some selected results from water quality surveillance conducted by the U.S. Geological Survey (USGS) as one component of the RMP. We present results as lessons about how the Bay works as a complex dynamic system, and we show how these lessons are relevant to the broad RMP objectives supporting Bay protection and management.