The overwintering habitat use of shortnose sturgeon (Acipenser brevirostrum) was investigated from January to March 2005 in the upper Kennebecasis River, New Brunswick, Canada, using a novel underwater video camera system and modeling approach. Following a random sampling procedure, 187 holes were drilled into the ice, and 234 sturgeon were counted and video-recorded. We found that sturgeon concentrated in a 2 ha area at the confluence of the Kennebecasis and Hammond rivers on a flat sandy substrate at a depth of 3.1–6.9 m. Generalized linear models were developed to describe the relationship of shortnose sturgeon density and habitat variables. The model indicated that the shortnose sturgeon had significant preference to deeper areas within this region. The total abundance of shortnose sturgeon in the area was estimated to be 4836 ± 69 (mean ± standard error) using the ordinary kriging method to interpolate sturgeon density at unsampled sites. This overwintering habitat of shortnose sturgeon can be defined as critical habitat following the identification policies of the Canadian Species at Risk Act (SARA).