Antarctic subglacial lakes can play an important role in ice sheet dynamics, biology, geology, and oceanography, but it is difficult to definitively constrain their character and locations. Subglacial lake locations are related to factors including heat flux, ice surface slope, ice thickness, and bed topography, though these relationships are not fully quantified. Bed topography is particularly important for determining where water flows and accumulates, but digital elevation models of the ice sheet bed rely on interpolation and are unrealistically smooth, biasing estimates of subglacial lake location and surface area. To address this issue, we use geostatistical methods to simulate realistically rough bed topography. We use our simulated topography to predict subglacial lake distribution across the continent using a binomial logistic regression, which uses physical parameters and known lake locations to calculate the probabilities of lake occurrences. Our results suggest that topography models interpolated without appropriate geostatistics overestimate subglacial lake surface area and that total lake surface area is lower than previously predicted. We find that radar‐detected lakes are more likely to occur in the interior of East Antarctica, while altimetry‐detected (active) lakes are expected to be found in West Antarctica and near the grounding line. We observe that radar‐detected lakes have a high correlation with heat flux and ice thickness, while active lakes are associated with higher ice velocity.