Flint Creek is part of the Oswego River drainage basin, which ultimately drains to Lake Ontario.

It then flows through the hamlets of Potter, Gorham, and Seneca Castle, and ends in the village of Phelps where it joins the Canandaigua Outlet.

The creek was known by the Iroquois as Ax-o-quent-a or Ah-ta-gweh-da-ga, the latter name being translated as "flint stone", with its origins in the Cayuga or Seneca dialect.

[3] A very large area of muckland used for vegetable crop farming was created by clearing and draining a swamp along Flint Creek located in the town of Potter.

A part of Flint Creek known as Phelps Run is used for whitewater rafting and kayaking and has class II, III, and IV rapids.