We conducted at-sea experiments using separation chemistry and an inductively coupled plasma mass spectrometer to rapidly measure, in real time, trace element concentrations in the surface water of the San Diego Bay and the adjacent coastal ocean. The survey shows that surface water in the San Diego Bay is clearly enriched in Mn, Ni, Cu, Zn, Cd, and FDOM with respect to the coastal ocean. Trace element enrichment patterns were used to identify bay water as it enters the coastal ocean during tidal pumping. Quantifying the spatial distribution and temporal flux of pollutant trace elements are important steps in understanding coastal biogeochemical processes.