Conservation planning of coastal ecosystems is improved by quantitative data on human activities and marine habitats, though is challenging in artisanal fisheries due to their characteristics of multiple species, gears and landing sites. Small-scale coastal fisheries in northern Mozambique were quantified using a multi-faceted approach, to inform area-based conservation and fisheries management. Fishers captured 153 taxa using eleven different fishing gears with a high proportion of gleaning. The most prevalent gear was the mosquito net (27%), largely used by women, followed by gleaning, handline and spear (12–15%), but with high inter-fishing ground variability. Median (interquatile range) catch rates ranged from 7.0 (3.4, 15.1) kg fisher−1 trip−1 (handlines) to 2.3 (1.6, 4.5) kg fisher−1 trip−1 (mosquito nets), which represent relatively high catch rates for eastern Africa. Knowledge of the complex spatial variability in these fisheries can contribute to conservation planning by minimizing opportunity costs while maximizing conservation benefits.