We used acoustic telemetry to assess site fidelity, movement patterns, and habitat use within the lower Maeklong River, Thailand, by 22 giant freshwater whipray Urogymnus polylepis. This study is the first of its kind for this rare, endangered species, and it begins to fill critical information gaps about its ecology and life history. Study animals were tagged subcutaneously in the dorsal area with acoustic transmitters and tracked for 12 months using a fixed array of eight receivers. Receivers were positioned within an 18 rkm section of the Maeklong, starting approximately 4 rkm upstream from the mouth. We calculated individual residency indices, tracked longitudinal movements, and assessed annual and seasonal patterns of site use. We also investigated spatial use patterns, diel activity patterns, and relationships of temperature and site fidelity. We detected 86% of our tagged whiprays, 53% of which were detected for the majority of the study period. Whiprays exhibited high site fidelity across seasons. Individuals made long longitudinal movements within the site for much of the study period but seemed to remain closer to the estuary during the second half of the rainy season and early winter. All receivers had large numbers of detections, but upstream receivers were visited for longer time durations than downstream receivers. A receiver in the middle of the study area had the highest detection rate, but low detection durations, suggesting that this receiver is in a migration corridor. A mix of immature and mature males and females was present in the site throughout the study period, suggesting that this area is not exclusively a breeding or nursery site. However, the high site fidelity suggests that this is an important aggregation site for the species. Effective conservation measures may include conservation zones and a shrimp reintroduction program upstream, ensuring fish passage through the middle of the site, and regulating traffic and pollution downstream. We found acoustic telemetry to be an effective study method and encourage its use to improve understanding of the giant freshwater whipray.