Understanding drivers of habitat use and selection of mobile species is critical for understanding the impacts of climate change and formulating management plans. Eastern Beaufort Sea beluga whales Delphinapterus leucas form large summering aggregations in the warm, fresh waters of the Mackenzie Estuary, Northwest Territories, Canada; however, the environmental factors driving spatial and temporal patterns of habitat use within the estuary are not fully understood. We used passive acoustic monitoring to record beluga presence during their summer aggregation (June-August) at known congregation areas and locations with unique oceanographic features in Kugmallit Bay in the Mackenzie River Estuary, while simultaneously recording environmental and oceanographic data. The effectiveness of hydrophones at determining beluga presence/absence was validated using shore-based observations. Multiple logistic regression was used to assess the influence of environmental conditions on presence/absence of belugas. Results indicate that temporal patterns of habitat use varied by location, and were influenced by environmental conditions such as temperature, salinity, and wind speed. Belugas did not frequent commonly used locations during periods with high-speed winds and moved farther into the estuary during periods of cold oceanic influxes. This study provides support for hypotheses that belugas use the location for moulting or to provide a thermal advantage for young belugas. This information can be used to inform decisions by northern communities and policy makers, thus aiding in management of the Beaufort Sea beluga population.