The transition from marine to freshwater life in the threespine stickleback (Gasterosteus aculeatus) is accompanied by complex morphological changes—including reduction in bony armor and change in body shape—but experimental evidence for the selective agents behind these evolutionary transitions is sparse. We investigated whether selection by predatory fish affects threespine stickleback morphology differentially when refuge is absent (pelagic lifestyle—ancestral condition) or present (benthic lifestyle—derived condition). Our results show that selection favors low numbers of lateral plates in habitats with refuge, whereas fully plated individuals have a selective advantage in habitats without refuge. We also found that a decrease in the length of the caudal peduncle increased survival probability, irrespective of habitat. The effect of spine lengths on survival was evident only in a multivariate analysis of selection, implying that it is essential to account for phenotypic and genetic correlations between traits before drawing conclusions about the effects of selection on single traits. Apart from uncovering targets and patterns of predator-induced selection on threespine stickleback morphology, our results provide direct evidence to support the hypothesis that differences in antipredator strategies in pelagic versus benthic sticklebacks could play a role in the repeated, independent cases of plate number reduction following freshwater colonization in this species.