This study describes the seasonal diet composition of the Pacific harbor seal (Phoca vitulina) in two estuaries, Padilla Bay and Drayton Harbor, in the central Salish Sea. Prey remains were recovered from harbor seal fecal samples (scats) collected at haul-out sites during spring and summer/fall in 2006. Top prey taxa (≥ 25% frequency of occurrence) were compared between seasons, estuaries, and between estuarine and non-estuarine haul-out sites. Overall, prey from at least 26 taxonomic families were identified in 198 harbor seal scats. In Padilla Bay, the most common prey were gunnel (family Pholidae; 88.6%), snake prickleback (Lumpenus sagitta; 59.1%), Pacific staghorn sculpin (Leptocottus armatus; 50.0%), and shiner perch (Cymatogaster aggregata; 47.7%). Threespine stickleback (Gasterosteus aculeatus; 95.5%) and Pacific herring (Clupea pallasi; 83.1%) were the most frequently consumed species in Drayton Harbor; shiner perch, snake prickleback, mammal, and Pacific staghorn sculpin also each occurred in ≥ 50% of samples from at least one season. Occurrences of top prey taxa varied by season, estuary, and habitat type. Diet composition suggests that harbor seals in Padilla Bay and Drayton Harbor foraged primarily within estuarine habitats such as those found near the haul-out sites. Temporal and spatial variations in diet appeared to reflect differences in the availability of prey taxa. This study also identifies mammals as a potentially novel prey item for harbor seals in Drayton Harbor.