Bontecou Lake straddles the drainage divide between the Wappinger Creek watershed to the west and the Tenmile River.

This was attributed to a harsh winter that killed aquatic plant life in the shallow reservoir, depleting water oxygen levels.

[8][9] The NYSDEC also monitors and regulates land usage in a 320-acre (130 ha) tract surrounding and including the lake, as directed by the New York State Freshwater Wetlands Act of 1975.

[11] Today, the lake and swamp are home to hundreds of Canada geese year-round, with many thousands using the area as a stop-over point during migration periods.

[11] Dead trees extending above the surface of the water quickly made this a preferred breeding ground for great blue herons,[3] which continue to nest on the eastern side of the lake.