Mission Bay Park was developed from the 1940s through the 1960s using a tidal marsh named “False Bay”. The San Diego River had historically shifted its outlet between San Diego Bay and False Bay, until 1852 when the United States Army constructed the first dike along the south side of the river to prevent it from shifting back to San Diego Bay. The San Diego River is now constrained on both the north and the south by levees and it no longer drains to the ocean through what is now called Mission Bay.

Mission Bay gets freshwater input from Rose Creek in the Northeast corner, and Tecolote Creek in the Southeast corner near Fiesta Island. The Rose Creek Watershed drains a 23,427-acre or 36-square mile area into Mission Bay. The main natural features of this watershed include Rose and San Clemente Canyons and their tributary canyons, including Stevenson and Lakehurst Canyons. This watershed transects portions of Scripps Ranch, Mira Mesa, Kearny Mesa, La Jolla, Pacific Beach, Clairemont Mesa, and almost the entirety of University City. Tecolote Creek drains an area of about 10 square miles mostly in Clairmont, Clairemont Mesa, Linda Vista, and Bay Park via Tecolote Canyon and its tributary canyons.

Most of the marsh and intertidal area in False Bay was destroyed to create the landforms of Mission Bay Park, which now is almost entirely man-made. There are a few small areas remaining in a more natural state, most notably the Kendall-Frost Reserve & Northern Wildlife Preserve. Other natural areas include Mariner’s Point, Perez Cove, Tecolote Creek, Fiesta Island, and Famosa Slough Wildlife Preserve. A portion of the Flood Control Channel between the levees that confine the river is designated as the Southern Wildlife Preserve.