The Fishing Creek watershed has been affected by glaciation, which has left a glacial till near the source and glacial outwash in the lower parts of the watershed. The watershed lies in two major geological regions: the Deep Valley section of the Allegheny Plateau and the Susquehanna Lowlands Section. The Allegheny Plateau lies in the upper reaches of the watershed and is characterized by deep valleys and rounded mountains with elevations of around . The Susquehanna Lowlands section is characterized by linear ridges of moderate elevation and valleys less steep than those of the Deep Valley region. There are also flood plains along the creek. Near its mouth, it cuts through Montour Ridge, and a basalt-containing section of the Catskill Formation extends to the creek's banks in Hemlock Township. Other rock formations along the banks include the Clinton Formation, the Selena Formation, the Lower Helderburg Formation, and the Hamilton Formation. There is a terminal moraine, which crosses the creek near Benton.