Historic habitat conditions can affect contemporary communities and populations, but most studies of historic habitat are based on the reduction in habitat extent or connectivity. Little is known about the effects of historic habitat on contemporary species distributions when historic habitat has been nearly completely removed, but species persist in a highly altered landscape. More than 93% of the historic wetlands in the Central Valley of California, USA, have been drained and converted to agricultural and other uses, but agricultural wetlands, such as rice and its supporting infrastructure of canals, allow some species to persist. Little is known about the distribution of giant garter snakes Thamnophis gigas, a rare aquatic snake species inhabiting this predominantly agricultural landscape, or the variables that affect where this species occurs. We used occupancy modeling to examine the distribution of giant garter snakes at the landscape scale in the Sacramento Valley (northern portion of the Central Valley) of California, with an emphasis on the relative strength of historic and contemporary variables (landscape-scale habitat, local microhabitat, vegetation composition and relative prey counts) for predicting giant garter snake occurrence. Proximity to historic marsh best explained variation in the probability of occurrence of giant garter snakes at the landscape scale, with greater probability of occurrence near historic marsh. We suspect that the importance of distance to historic marsh represents dispersal limitations of giant garter snakes. These results suggest that preserving and restoring areas near historic marsh, and minimizing activities that reduce the extent of marsh or marsh-like (e.g. rice agriculture, canal) habitats near historic marsh may be advantageous to giant garter snakes.