A mass balance model was applied to simulate the long-term fate of PAHs in San Francisco Bay. The model treats the Bay as a single box with interacting water and sediment compartments, and includes loading, volatilization, outflow to the ocean, degradation, and burial in deep sediment. The estimated time required for loss of one-half of the mass in the Bay in the absence of loading ranged from 20 d for naphthalene to 5 yr for benzo(b)fluoranthene. Uncertainty analysis using Monte Carlo simulation indicated a high degree of influence and uncertainty for degradation rates, suggesting that improved estimates of degradation would significantly improve the predictive ability of the model. A comparison of model calculations to literature values suggested that external PAH loading to San Francisco Bay was at or above previous estimates of 3600 kgyr(-1), and that degradation in the Bay was within the range of commonly published estimates for high molecular weight PAHs (4.0 x 10(-5) to 4.0 x 10(-4)d(-1)).