The town is located at the western edge of the Des Moines Lobe, the most recently glaciated section of Iowa. The Des Moines Lobe is part of the prairie pothole region of the Midwest. The topography is irregular in its gently rolling terrain. Wetlands, glacial erratics, concentric bands of ridges, and large flat areas characterize the land surrounding Fonda. In its natural state, the land is poorly drained, although humans have added an extensive network of tiles to move water from the potholes to local tributaries. The tiles surrounding Fonda empty into Big Cedar Creek, a tributary of the Raccoon River. This waterway, which underwent channelization in the early 1900s, flows past the town on its west end. Evidence of its winding original path still exists, particularly in the Fonda Golf Course and in the schoolyard behind Our Lady of Good Counsel Catholic Church.