Unlike the other Fraser Valley municipalities Mission is mostly forested upland with only small floodplains lining the
shore of the Fraser River,
The municipality is bisected by the lower reaches of the Stave River, which consists mostly of the lakewaters of two hydroelectric reservoirs, Stave Lake and Hayward Lake. Although the vast majority of the population of Mission lives well to the east of the Stave, over 50% of the municipality is west and north of that river. A small portion of the lower Stave still runs free in its last two miles before its confluence with the Fraser at Ruskin, which is on the border with the larger municipality of Maple Ridge to the west. This hydroelectric system was the largest hydroelectric project in southwestern British Columbia until the 1950s and was built by the British Columbia Electric Railway (BCER) to provide power to the electric street railway and interurban system in Vancouver.
The eastern boundary of the municipality roughly coincides with the division between the Mission upland and the alluvial floodplain of Hatzic Prairie, which resembles much of the rest of the Fraser Valley Lowland. The unincorporated communities from Hatzic eastwards to Deroche are part of the social and commercial matrix centred on Mission but have never joined the municipality; their local societies are built on dairy, berry and corn farming as well as a large First Nations community at Lakahamen on Nicomen Island.