[5] Predictably, given its northern latitude, Whapmagoostui has a subarctic climate (Dfc) under the Köppen climate classification, but strongly modified by its location on the southeastern (predominantly windward) shore of Hudson Bay, particularly from May/June through November, the primary season when Hudson Bay's surface is unfrozen, i.e. open water.

Marie, Michigan), in spring and early summer, water temperatures are cooler than those of surrounding land areas, encouraging low clouds and fog, but also stable conditions and less precipitation.

In Whapmagoostui, this pattern means average monthly precipitation peaks in September – when increasingly cold air masses passing eastward and southeastward across the open waters of Hudson Bay are warmed and destabilized by their over-water passage, producing thick clouds and frequent, often-heavy instability rain (and from October to December, snow) showers.

From late November into December, Hudson Bay freezes, and by January, its frozen surface provides little modification to Arctic air masses, and less moisture, i.e. snow, to Whapmagoostui.

Considering its marine position on the 55th parallel, the climate is extremely cold when compared with cities like Glasgow and Copenhagen in northern Europe and Chinook-affected areas further to the west in Canada's interior.