Church Mountain is located in the marine west coast climate zone of western North America.

[4] Most weather fronts originate in the Pacific Ocean, and travel northeast toward the Cascade Mountains.

As a result, the west side of the North Cascades experiences high precipitation, especially during the winter months in the form of snowfall.

[4] Due to its temperate climate and proximity to the Pacific Ocean, areas west of the Cascade Crest very rarely experience temperatures below 0 °F (−18 °C) or above 80 °F (27 °C).

Precipitation runoff from the mountain drains into tributaries of the Nooksack River.