1. Despite the giant mottled eel Anguilla marmorata being a widely distributed and locally exploited species throughout the Indo Pacific region, understanding of its life history, behaviour and movement ecology remains limited.2. Knowledge of animal spatial ecology is essential for the effective design and siting of aquatic protected areas. In the current study, acoustic telemetry was used to quantify residence and explore the activity patterns and behaviour of A. marmorata (n = 68) in two freshwater protected areas (FPAs) for the first time in the Cagayan River Basin, Philippines.3. The results demonstrated that FPAs of only 1 km length provided refuge for A. marmorata for an average of 25-26% of the tracked period. Residence and activity patterns varied with habitat type. In pool and riffle habitat, activity reduced with increased river flow, and eel, particularly larger individuals, were more strongly nocturnal than those in the deep pooled, slow flowing habitat.Typhoon events displaced many individuals, particularly in the pool and riffle habitat, with only 3% returning to the FPA within the study. 4. Findings are discussed within the context of selecting FPA sites to optimize eel protection within catchments experiencing high non-selective fisheries exploitation and other threats.