The St. Lawrence Estuary (Québec, Canada) was the birthplace of organised whale watching activities on the east coast of North America. Initially, fin whales (Balaenoptera physalus) were the main target species. The creation of the Saguenay–St. Lawrence Marine Park enabled to regulate whale watching activities in the area and to adopt specific regulations. For management purposes, a sampling protocol was developed to monitor the activity. Data collected aboard large boats (> 50 passengers) during 1186 excursions departing from Tadoussac from 1994 to 2017 were analysed to characterize the target species and territory use over time. Since 2001, the main target species has changed and a marked decrease in the local density of fin whales has been observed. The fin whale was the most targeted species during 15 of the 24 years, followed by the minke whale (Balaenoptera acutorostrata, 6 years) and the humpback whale (Megaptera novaeangliae, 3 years). A partitioning analysis allowed the identification of years with similar patterns based on the species observed and on spatial distribution variables. Long-term continuity of the sampling protocol, in conjunction with systematic monitoring, will help to better understand this ecosystem and ensure adaptive management and sustainable development of the whale watching activities.