Fisheries management faces numerous monitoring and enforcement challenges that are becoming more complex as fish stocks are depleted; and illegal, unregulated, and unreported fishing becomes more sophisticated. For remote island nations, the challenges are compounded by a loosely understood association of pelagic stocks to the ocean environment, and the tyranny of distance in monitoring and surveilling large exclusive economic zones (EEZ). An approach to ocean conservation is establishing protected areas, with the Pacific island nation of Palau as a leader with the recently established National Marine Sanctuary, which closes 80% of their EEZ to commercial fishing in 2020. Here we present an EEZ-wide analysis of Palau commercial fishing over a 6-year period (2011-2016), and develop a system for predicting fishing activity accounting for oceanic variables, climate indices, and vessel flag. Linking pelagic habitat to fishing activity provides high-resolution decision aids for management, highlighting the need for EEZ-specific analyses in addressing fisheries.