The area is underlain by sedimentary rocks, including shales, sandstones, and limestones, formed roughly 400 million years ago, during the Devonian period. There are four major groups in the bedrock of Tompkins County including the Hamilton, Genesee, Sonyea, and West Falls Groups. Within the Fall Creek watershed, the bedrock consists predominantly of shales in the valleys; while the hilltops and ridges are dominated by more erosion-resistant sandstones and siltstones. The exposed layers of sedimentary bedrock visible in the Fall Creek Gorge are mostly the Genesee Group, which is comprised of limestone, shale, and siltstone exposed at elevations of 400 to 1000 feet. Within the Genesee group is the Ithaca Formation, which is visible in the lower Fall Creek Gorge. At Ithaca Falls the fossiliferous rock outcrops have guide fossils, brachiopods such as Spirifera laevis, used to identify the base of the Ithaca Formation. The fossils of this thin stratum are so distinctive that they are used as a geological marker to date and identify this layer in the rock column.
The Fall Creek watershed, and indeed the Ithaca area, is characterized by high, flat-topped, steep-sided hills that are remnants of the ancient Allegheny plateau with valleys subsequently widened and made more steep-sided by the glaciers.
Fall Creek Gorge runs from Triphammer Falls at Beebe Lake Dam to Lake Street below Ithaca Falls, and is characterized by forested and rocky slopes and steep cliffs. Downstream of Ithaca Falls, the terrain levels out as Fall Creek flows into Cayuga Lake. The creek flows over a series of waterfalls as it flows between the steep cliffs of the gorge. Elevation drops from 813 feet at Beebe Lake to 382 feet below Ithaca Falls. The steep slopes occur from Beebe Dam to just past Ithaca Falls, while downstream (Ithaca Falls to Cayuga Lake), Fall Creek flows through the flat floodplain associated with Cayuga Lake.
Theforests on the dry gorge crests and south-facing slopes between Beele Lake and Ithaca Falls are Appalachian oak-hickory forest. Chestnut oak (Quercus montana) is abundant on the dry, rocky outcrops. These forests are dominated by chestnut oak, red oak (Quercus rubra), black oak (Quercus velutina), and white oak (Quercus alba), while shagbark hickory (Carya ovata) and pignut hickory (Carya glabra) are also present. Old-growth forests with trees well over 200 years old are found within Fall Creek Gorge and around Beebe Lake.
The cool, north-facing slopes have hemlock-northern hardwoods forest, where eastern hemlock (Tsuga canadensis)is often abundant. The lower slopes and gorge bottoms have beech-maple mesic forest and maple-basswood rich mesic forest. Sugar maple (Acer saccharum), basswood (Tilia americana), white ash (Fraxinus americana), yellow birch (Betula allegheniensis) red oak and tuliptree (Liriodendron tulipifera) are characteristic species here.
Fall Creek supports exceptionally diverse aquatic and benthic macroinvertebrate communities that include unusually many higher taxonomic groups. This is indicative of very high environmental quality.