Agricultural conversion is one of the most prevalent anthropogenic uses on the terrestrial earth. Persistence of organisms in such landscapes is thought to be related to species-specific characteristics such as life history traits and dispersal distance. In an agricultural landscape in California, we examined local (farm-level) and landscape variables associated with nesting preferences of native ground-nesting bees. Compared to the known ground-nesting visitors to crops, bee community nesting on farms was depauperate. Further, more abundant and diverse communities of bees were found nesting at farms with patches of natural habitat near by than farms that were far away from natural habitat. Species responded differently to soil conditions created by farming practices, but the variability in nesting bee abundance was lower in farms near natural habitat than farms far from natural habitat. These findings suggest that most bee species are affected adversely but to varying degrees by agricultural intensification, and that natural habitats may buffer against the bee population variability in agricultural landscape. We present source/sink dynamics and resource limitations as possible explanations for the observed patterns.