Three paleoecological studies were conducted on five lagoons and marshes in San Diego County in 1973–1975 and initial results were published in 1976. This paper integrates the earlier results with new palynological evidence, microfossil, and sedimentological data to provide a regional perspective of lagoon, salt-marsh, and climate changes in southern California over the past 8000 years. Foraminiferal species are illustrated and a revised taxonomy is presented. Ostracodes in the surface samples and boreholes of this region are illustrated for the first time.

Surface sample data show the relation between microfossil faunal assemblages, modern salinity, tidal exchange, water depth, and salt-marsh elevation in open lagoons at Tijuana estuary, San Diego and Mission bays, and Agua Hedionda, and for hypersaline-to-brackish marshes in the Los Peñasquitos wetlands. Drillhole lithofacies in Los Peñasquitos, Tijuana, and Mission Bay marshes were dated with seven radiocarbon ages in addition to those published in 1976. The microfossil surface sample data were used to interpret the drillhole records, showing the paleoecological evolution of the wetlands and the variation within and between lagoons located less than 40 km apart. Abundances of planktonic and other nearshore foraminifera show that Los Peñasquitos lagoon was much more open in the mid-Holocene compared to today. Palynological data provide the first documentation of mangrove migration as far north as San Diego in the mid-Holocene, which implies warmer winters and wetter summers at that time. Palynostratigraphic data also permit refined timing of recent changes (past 300 years) in lagoonal environments based on use of historical dates for introduced plant species.

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