[3] San Felipe Lake is the terminus of Pacheco Creek, which drains the western slope of California's Diablo Range.

The Soap Lake Floodplain was historically a mix of seasonal and perennial, fresh and saline wetlands connected by swales and sloughs.

[13] San Felipe Lake hosts runs of the federally threatened South-Central California Coast steelhead trout (Oncorhynchus mykiss) distinct population segment (DPS).

[13] In 1912, Stanford University ichthyologist John Otterbein Snyder recorded reports of Chinook salmon (Oncorhynchus tschawytscha) in the Pajaro River watershed.

The current management of natural areas surrounding San Felipe Lake is geared towards ranching and agriculture, which is associated with unnaturally-timed summer water releases, discing (for agriculture), cattle trampling and soil compaction, that negatively impacts the fragile wetlands and adjacent alkaline grassland that fringe San Felipe Lake and its flood plain.