Tropical macroalgal meadows are emerging as an important habitat for numerous fish populations and communities. Recent research has indicated that the abundance of macroalgal-associated fishes is correlated to different aspects of macroalgal canopy structure, such as canopy cover, height, and/or density. Our study aimed to explore a possible mechanism for these correlations, by exploring the foraging microhabitat preferences of 16 invertivorous fish species occupying macroalgal meadows at Ningaloo Reef, Western Australia. Instantaneous focal censuses of searching and feeding behaviour by these fishes was compared to microhabitat availability within each meadow using selectivity analysis. Despite sharing a similar trophic guild, we found these invertivorous fishes tended to diverge in their microhabitat use – some species preferred foraging within the canopy-forming macroalgae (Sargassum), while other species targeted abiotic substrata (sand, pavement, and/or rubble); most fishes avoided foraging within understory macroalgae (Lobophora, Dictyopteris). In revealing these microhabitat preferences among macroalgal-associated fishes, we find a behavioural mechanism that could explain why fishes respond to changes in different aspects of macroalgal canopy habitat structure over space and time.