It is located 82 kilometres (51 mi) south of the border to the Northwest Territories, the community is astride the Fond du Lac River.

The hospital, located on reserve land (Chicken 224) of the Black Lake Dene Nation adjacent to Stony Rapids, is part of the Athabasca Health Authority.

[8][9] Stony Rapids has a subarctic climate (Köppen Dfc) with long, severe winters and short, mild to warm summers.

Unlike towns further west, temperature above 0 °C (32 °F) are very rare during winter, occurring on average only 1.5 times from December to February.

The average frost-free period is eighty-one days from 9 June to 30 August, though temperatures below 0 °C (32 °F) have occurred a handful of times in July.