The San Clemete Watershed covers an area of 31.8 square miles in the southernmost corner of Orange County. It includes the City of San Clemente, a small portion of the City of San Juan Capistrano, and a large portion of unincorporated territory. Its main tributaries are Prima Deshecha Canada and Segunda Deshecha Canada.

The Regional Water Quality Control Board defines this area as two watersheds: San Clemente Coastal Streams and San Mateo Creek.