Three main rivers that run through Jericho: Brown’s River, the Lee River, and Mill Brook. While Mill Brook flows into the Winooski River, The Lee and Brown’s Rivers flow instead into the Lamoille River. All water from Jericho eventually flows into Lake Champlain. With mountains to the east of Jericho and the Champlain valley to the west, water in Jericho all follows a roughly westerly direction, although there is a great deal of variation on a finer scale. The Winooski River, which borders the town to the west, actually flows to the North through this area.

There are also a number of wetland complexes within the town boundaries, including a significant area near Nashville Road, an easily-visible set in the center of town behind the village store, and another complex along Skunk Hollow Road. These wetlands aid the town in a number of ways. Not only do they serve as habitat for a large diversity of wildlife; they also function as water quality check stations, filtering pollutants and chemicals from runoff that enters them.