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Marine protected areas (MPAs) can contribute to protecting biodiversity and managing ocean activities, including fishing. There is, however, limited evidence of ecological responses to blue water MPAs. We conducted the first comprehensive evaluation of impacts on fisheries production and ecological responses to pelagic MPAs of the Pacific Remote Islands Marine National Monument. A Bayesian time series-based counterfactual modelling approach using fishery-dependent data was used to compare the temporal response in the MPAs to three reference regions for standardized catch rates, lengths, trophic level of the catch and species diversity. Catch rates of bigeye tuna, the main target species (Kingman/Palmyra MPA, causal effect probability >99% of an 84% reduction; 95% credible interval: -143%, -25%), and blue shark (Johnston MPAs, causal effect probability >95%) were significantly lower and longnose lancetfish significantly higher (Johnston MPAs, causal effect probability >95%) than predicted had the MPAs not been established, possibly from closing areas near shallow features, which aggregate pelagic predators, and from 'fishing-the-line'. There were no apparent causal impacts of the MPAs on species diversity, lengths and trophic level of the catch, perhaps because the MPAs were young, were too small, did not contain critical habitat for specific life-history stages, had been lightly exploited or experienced fishing-the-line. We also assessed model-standardized catch rates for species of conservation concern and mean trophic level of the catch within and outside of MPAs. Displaced effort produced multi-species conflicts: MPAs protect bycatch hotspots and hotspots of bycatch-to-target catch ratios for some at-risk species, but coldspots for others. Mean trophic level of the catch was significantly higher around MPAs, likely due to the aggregating effect of the shallow features and there having been light fishing pressure within MPAs. These findings demonstrate how exploring a wide range of ecological responses supports evidence-based evaluations of blue water MPAs.