Even though a channel has been cut through the foliage, paddling trips on the creek can be difficult due to a number of log jams from fallen trees as a result of ice storms which hit the greater Rochester area in 1991 and 2003.

From the confluence, Ganargua Creek flows north and east through the western end of the town of Farmington, including passing under the New York State Thruway, before entering Wayne County.

The 18-mile (29-kilometer) northern section of Ganargua Creek, known as the "Lower" on watershed documents, begins in the Wayne County town of Palmyra at a spillway off the Erie Canal near Swifts Landing Park west of Galloway Road along NY Route 31.

It will pass just north of the village of Newark and continue northeast along the Ontario Midland Railroad line to just south of the community of Fairville Station at Norsen Bridge Park.

Ganargua Creek will then meander its way back southeast along Bauer-Van Wickle Road and Layton Street into the town and hamlet of Lyons where it will finally enter the Erie Canal at Miller's Marina near Abbey Park west of Lock #27.

Mormonism founder Joseph Smith also had an interest in the creek after hearing a speech from Seneca Indian Chief Red Jacket at Palmyra in 1822.

Before the Erie Canal was constructed in 1817, Ganargua Creek originally met the Canandaigua Outlet in Lyons to form the Clyde River.