Analyses of sea level and current-meter data using digital filters and a variety of statistical methods show a variety of phenomena related to non-local coastal forcing and local tidal forcing in the northern reach of San Francisco Bay, a partially mixed estuary. Low-frequency variations in sea level are dominated by non-local variations in coastal sea level and also show a smaller influence from tidally induced fortnightly sea level variations. Low-frequency currents demonstrate a gravitational circulation which is modified by changes in tidal-current speed over the spring-neap tidal cycle. Transients in gravitational circulation induce internal oscillations with periods of two to four days.