Copper-based antifouling paint has become an environmental concern in San Diego Bay. High copper concentrations have been observed in San Diego Bay and its marinas. Pier 32 Marina is the newest built marina in San Diego Bay in the last 15 years. The objectives of this study were to (i) gather representative copper and zinc surface water column chemistry data before and after the introduction of boats in Pier 32 Marina, (ii) compare the copper and zinc concentrations in Pier 32 Marina to observed concentrations in Shelter Island Yacht Basin (SIYB), and (iii) develop a box model to analyze the dominant processes that control steady state copper concentrations in Pier 32 Marina. Methods used included (i) collection of surface water from six sampling locations in Pier 32 Marina and five sampling locations in SIYB, (ii) paired t-test and t-test statistical analyses, (iii) and an estimation of the copper loading, residence time, and steady state concentrations. Copper concentrations exceeded the California Toxics Rule (CTR) numeric targets of 4.8 _g/L and 3.1 _g/L in Pier 32 Marina when boat occupancy ranged from 64-77%. Zinc concentrations remained below the CTR numeric targets of 90 _g/L and 81 _g/L during the entire study. Based on t-test analysis there was a significant difference (p < 0.05) among the four marina sample locations and two reference sample locations. Copper loading rose linearly without consideration of tidal flushing to 125 kg based on 192 boats at the end of the study period. The residence time in Pier 32 Marina ranged from 2-2.8 days compared to 1.8-4.7 days in SIYB. The box model estimated that steady state concentrations ranged from 3.83-5.37 _g/L in Pier 32 Marina and from 3.07-8.16 _g/L in SIYB. Tidal flushing was identified as a primary driver so that copper does not accumulate linearly. It is suggested that the box model with flushing and no sedimentation provided reasonable predictions in steady state concentrations in tidally-influenced marinas.