We collected data on the distribution of Balaenoptera physalus (Finback Whale), Balaenoptera acutorostrata (Minke Whale), and Megaptera novaeangliae (Humpback Whale), in the Quoddy region of the Bay of Fundy, Canada, from a whale-watching vessel during commercial tours from 2006 to 2012. Sightings were non-random between species and showed clumped distributions over the study area: Finback Whales (χ² = 2454.03, df = 7, P < 0.005), Minke Whales (χ² = 3488.24, df = 7, P < 0.005), and Humpback Whales (χ² = 301.784, df = 7, P < 0.005). Minke Whales were most frequently sighted in Head Harbour Passage, high concentrations of Finback Whales were most frequently sighted off Blacks Harbour, and Humpback Whale sightings were highest around The Wolves. It appears that the whales aggregate in response to physical and biological features of the environment, such as depth, bottom topography, and fine-scale oceanographic features that enable foraging. Oceanographic features such as tidal state and temperature also influence the distribution of whales by aggregating their common prey species in high concentrations.