Aetna Township is situated in the southern tier of Mecosta County in Michigan's Lower Peninsula. The physical geography is dominated by glacial plains, a legacy of the last Ice Age, which left behind fertile soils interspersed with sand and gravel deposits.
The most prominent natural feature is the Little Muskegon River, which flows westward through the township and the village of Morley before eventually joining the broader Muskegon River system. The landscape features a mix of active farmlands, secondary-growth deciduous and coniferous forests, and intermittent wetland areas.