The recovery of many cetacean species coincides spatially and temporally with intensifying anthropogenic threats. We undertook multi-year systematic surveys to quantify seasonal abundance and document the distribution of at-risk cetaceans, which is needed to assess the impacts of increasing human activities in the Canadian portions of the southern Salish Sea and Swiftsure Bank. We completed 21 line-transect surveys encompassing 5346 km of visual effort from September 2020 to December 2022 and collected 1514 sightings of five cetacean species using distance sampling protocols. Humpback whales, harbor porpoises, and Dall's porpoises were the most sighted species and were present in the area year-round, with strong seasonal differences in their abundance and distribution. Estimated abundance of humpback whales was lowest in winter at 17 (95% CI: 11–26) and highest in fall at 416 (261–663). Harbor porpoise abundance was also lowest during winter at 606 (366–1006) and highest in fall at 1415 (975–2055). Dall's porpoise abundance was lowest in summer at 65 (38–112) and highest in winter at 333 (224–494). These estimates were not corrected for availability or perception bias; thus, they may underestimate true abundance to some extent. These seasonal patterns in abundance and distribution will inform threat assessment and mitigation for cetaceans in this area of high and increasing vessel traffic.