AbstractDespite suffering dramatic declines due to habitat loss and overexploitation, tortoises and freshwater turtles in Southeast Asia remain understudied. Sustainable forest management offers a promising approach for advancing the conservation of threatened turtle populations. This study examines the effect of reduced impact logging (RIL), a sustainable forestry method, on 2 freshwater turtle species. We examined detectability patterns and habitat relationships for the threatened Malayan flat‐shelled turtle (Notochelys platynota) and the non‐threatened Malayan soft‐shelled turtle (Dogania subplana) in 8 streams within a commercial forest reserve between March and July 2019, in Sabah, Malaysian Borneo. Using single‐species occupancy models, we identified covariates associated with the detection and occupancy probabilities of these species across a post‐harvest recovery gradient (1–21 years since logging). Covariates used in the models were obtained directly from the field or from open‐source remote sensing data. Results for soft‐shelled turtles were inconclusive. In contrast, we found a negative association between monthly rainfall and flat‐shelled turtle detectability. The occupancy probability of flat‐shelled turtles was positively associated with greater distance from logging roads and higher stream flow accumulation. Occupancy probability for flat‐shelled turtles and soft‐shelled turtles was relatively high throughout the reserve (0.79 ± 0.1 [SD] and 0.57 ± 0.22, respectively). These results, suggest that appropriately managed forests, could serve as invaluable conservation areas for imperiled freshwater turtle species in the region.