Adaptation to different foraging resources is believed to be an important driving force of divergence between populations. Following colonization of freshwater, threespined sticklebacks (Gasterosteus aculeatus) have occupied and adapted to different types of aquatic niches. Adaptation to freshwater often involves, among other things, loss of lateral plates, shift to benthic resource exploitation, and change in body shape. Here, divergence in foraging behaviour and body shape is investigated among different lateral plate morphs coexisting in brackish water, and in a monomorphic population from a river habitat. Foraging behaviour was tested experimentally in the lab by observing fish that were offered benthic and pelagic prey simultaneously, while tracking the movements of the fish automatically. Shape differences were characterized using geometric morphometric Thin plate spline analysis. Significant and corresponding differences in foraging behaviour and shape were found between the plate morphs, and between sticklebacks from river and the lake. The results indicate ecological divergence towards benthic and pelagic habitat use between the plate morphs, resembling that of coexisting benthic-pelagic species pairs. This further suggests a possibility for evolution of ecologically based reproductive barriers between the coexisting morphs, although this remains to be investigated in more detail.