[6][7] The depressions forming Crystal, Pelican and Bass lakes appear to have been caused by the Double Point Slide, which covers an area of about 1.7 square miles (4.4 km2).

[7] Prior to geological research in the 1960s, the area was considered to be sufficiently stable for the United States Army to construct an underground artillery control facility within the North Point headland directly west of Pelican Lake in 1944.

[11] The lake is within the Southern Inverness Ridge region of the Point Reyes National Seashore, in an area of coastal scrub and grassland.

In this coastal zone there are open stands of coyote brush (Baccharis pilularis), often with native grasses such as California oatgrass (Danthonia californica) and purple needlegrass (Nassella pulchra).

[13][14] Pelican Lake is adjacent to the 86-acre (35 ha) Double Point Area of Special Biological Significance, established in 1974 primarily to protect the large population of harbor seals (Phoca vitulina) that raise pups on the beach between April and June each year.