Reeder Creek has its origins in the former Seneca Army Depot and flows north then west into Seneca Lake just north of Sampson State Park.  Reeder Creek watershed is made up of 60% forest and 31% agriculture, with a wetland area at its source.

Kashong Creek flows into the west shore of Seneca Lake about seven miles south of Geneva. It has a relatively large watershed area that makes up approximately 6% of the total Seneca Lake watershed area. Its watershed is roughly 83% agriculture and 15% forested land, and includes only very minimal residential or urban areas.

Keuka Outlet is the largest tributary to Seneca Lake, with its watershed area representing 35% of the Lake's total area. It is the sole outlet of Keuka Lake, and flows northeast from Penn Yan to Dresden, on the central western shore of Seneca Lake. Flow from Keuka Lake is controlled by gates in a dam at Penn Yan. The drainage area into the outlet, not including Keuka Lake, is 79% agriculture and 16% forested land. The outlet has a long history of mills and other industry on its shores, and has historically functioned as a canal for water transport between the two lakes.

Big Stream flows into the west shore of Seneca Lake at Glenora Point. It has a relatively large watershed that makes up approximately 7% of the total Seneca Lake watershed area. Its watershed is roughly 74% agriculture and 15% forested land, and it passes through the village of Dundee. 

Glen Eldridge is a small pristine stream on the southeast shore.

Catharine Creek is one of the major tributaries to Seneca Lake, encompassing approximately 31% of the total Seneca Lake watershed area. It originates in the Horseheads, NY area and flows north, into the southern tip of the Lake. It is by far the longest Seneca Lake tributary, with this watershed consisting of 49% agriculture and 45% forested areas.