Understanding the influence of heterogeneous marine landscapes on the movements of benthic megafauna is often hampered by limited spatial resolution and insufficient sample size. Here, we combined the benefits of seabed mapping, georeferenced trap arrays, and conventional tagging methods to quantify the effect of substrate on movements of the American lobster ( Homarus americanus ). In total, 21 848 lobsters were tagged, and movements were tracked among spatially referenced research and commercial traps. We found that lobster densities from diver surveys were highest on rocky habitat, but catch rates in traps were highest on unstructured sediment, resulting in traps on level bottom having a larger effective fishing area than traps on structurally complex habitat. Moreover, tag returns indicated that lobsters initially caught and released on sediment moved farther and faster than those initially caught in traps on rocky substrate. These observations are consistent with previous reports of the existence of a dichotomy of transient and resident lobsters in coastal populations, but the association of movement with habitat type was unknown. Our results indicate that field studies integrating conventional trapping, visual census, and tagging with seabed mapping can efficiently generate high-resolution information on habitat-related behavior of large samples of benthic organisms.