We use a combination of proxy records from a high-resolution analysis of sediments from Searsville Lake and adjacent Upper Lake Marsh and historical records to document over one and a half centuries of vegetation and socio-ecological change—relating to logging, agricultural land use change, dam construction, chemical applications, recreation, and other drivers—on the San Francisco Peninsula. A relatively open vegetation with minimal oak (Quercus) and coast redwood (Sequoia sempervirens) in the late 1850s reflects widespread logging and grazing during the nineteenth century. Forest and woodland expansion occurred in the early twentieth century, with forests composed of coast redwood and oak, among other taxa, as both logging and grazing declined. Invasive species include those associated with pasturage (Rumex, Plantago), landscape disturbance (Urtica, Amaranthaceae), planting for wood production and wind barriers (Eucalyptus), and agriculture. Agricultural species, including wheat, rye, and corn, were more common in the early twentieth century than subsequently. Wetland and aquatic pollen and fungal spores document a complex hydrological history, often associated with fluctuating water levels, application of algaecides, raising of Searsville Dam, and construction of a levee. By pairing the paleoecological and historical records of both lakes, we have been able to reconstruct the previously undocumented impacts of socio-ecological influences on this drainage, all of which overprinted known climate changes. Recognizing the ecological manifestations of these impacts puts into perspective the extent to which people have interacted with and transformed the environment in the transition into the Anthropocene.