Paleoenvironments of the Torrey Pines State Reserve were reconstructed from a 3600-yr core from Los Peñasquitos Lagoon using fossil pollen, spores, charcoal, chemical stratigraphy, particle size, and magnetic susceptibility. Late Holocene sediments were radiocarbon dated, while the historical sediments were dated using sediment chemistry, fossil pollen, and historical records. At 3600 yr B.P., the estuary was a brackish-water lagoon. By 2800 yr B.P., Poaceae (grass) pollen increased to high levels, suggesting that the rising level of the core site led to its colonization by Spartina foliosa (cord-grass), the lowest-elevation plant type within regional estuaries. An increase in pollen and spores of moisture-dependent species suggests a climate with more available moisture after 2600 yr B.P. This change is similar to that found 280 km to the north at 3250 yr B.P., implying that regional climate changes were time-transgressive from north to south. Increased postsettlement sediment input resulted from nineteenth-century land disturbances caused by grazing and fire. Sedimentation rates increased further in the twentieth century due to closure of the estuarine mouth. The endemic Pinus torreyana (Torrey pine) was present at the site throughout this 3600-yr interval but was less numerous prior to 2100 yr B.P. This history may have contributed to the low genetic diversity of this species.