San Pablo Bay, in northern San Francisco Bay, California, is an important wintering area for Greater (Aythya marila) and Lesser Scaup (A. affinis). We investigated variation in foraging behavior of scaup among five sites in San Pablo Bay, and whether such variation was related to densities of their main potential prey, the clams Potamocorbula amurensis and Macoma balthica. Time-activity budgets showed that scaup spent most of their time sleeping at some sites, and both sleeping and feeding at other sites, with females feeding more than males. In the first half of the observation period (12 January–5 February 2000), percent time spent feeding increased with increasing density of P. amurensis, but decreased with increasing density of M. balthica (diet studies have shown that scaup ate mostly P. amurensis and little or no M. balthica). Densities of M. balthica stayed about the same between fall and spring benthic samples, while densities of P. amurensis declined dramatically at most sites. In the second half of the observation period (7 February–3 March 2000), percent time feeding was no longer strongly related to P. amurensis densities, and dive durations increased by 14%. These changes probably reflected declines of P. amurensis, perhaps as affected by scaup predation. The large area of potential feeding habitat, and alternative prey elsewhere in the estuary, might have resulted in the low correlations between scaup behavior and prey densities in San Pablo Bay. These low correlations made it difficult to identify specific areas of prey concentrations important to scaup.