The Pinellas-Anclote watershed is located in the southwest portion of Pasco County with small portions extending into both Hillsborough and Pinellas County. The watershed is bordered by the Gulf of Mexico to the west, the Pithlachascotee River to the north, the Cypress Creek watershed to the east, and the Brooker Creek and Rocky-Bushy Creek watersheds to the south.
The Anclote River begins east of the Suncoast Parkway in the Southwest Florida Water Management District's Starkey Wilderness Preserve and the J.B. Starkey Wilderness Park and flows generally southwesterly towards the Gulf of Mexico. Tributaries that feed the river include Cross Cypress Branch, Sandy Branch, Duck Slough, and Holling Creek, as well as the south branch of the river itself. Lakes within the watershed include Ann, Dan, Frances, Geneva, Hiawatha, Minniola, Osceola, Salt, and Seminole. In the downstream portion of the watershed, close to where the Anclote River discharges to the Gulf of Mexico, are Kreamer, Tarpon, and Whitcomb bayous.
The Anclote River drains approximately 112 square miles of Pasco and northern Pinellas County through 24 river miles. The river is tidally affected for the lower 14 miles.