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Marine top predators such as seabirds are useful indicators of the integrated response of the marine ecosystem to environmental variability at different scales. Large-scale physical gradients constrain seabird habitat. Birds however respond behaviourally to physical heterogeneity at much smaller scales. Here, we use, for the first time, three-dimensional GPS tracking of a seabird, the great frigatebird (Fregata minor), in the Mozambique Channel. These data, which provide at the same time high-resolution vertical and horizontal positions, allow us to relate the behaviour of frigatebirds to the physical environment at the (sub-)mesoscale (10–100 km, days–weeks). Behavioural patterns are classified based on the birds’ vertical displacement (e.g. fast/slow ascents and descents), and are overlaid on maps of physical properties of the ocean–atmosphere interface, obtained by a nonlinear analysis of multi-satellite data. We …