A pregnancy imposes a heavy reproductive burden on females. Some live-bearing species have evolved reproductive adaptations to reduce this burden, which may influence their ability to use specific microhabitats. We investigate whether two such reproductive adaptations, placentation (embryo provisioning via a placenta) and superfetation (the ability to carry multiple broods at various developmental stages), influence microhabitat selection by five sympatric Costa Rican live-bearing fish species (family Poeciliidae). Theory predicts that placentation and superfetation should both reduce the reproductive burden of females during pregnancy, improve their body streamlining, and swimming performance, and consequently allow them to use more performance-demanding microhabitats. Here we apply underwater visual fish surveys to test a key prediction of this hypothesis, which is that the presence of these two reproductive adaptations is correlated with the use of microhabitats in the river that are characterised by a higher-flow velocity. Consistent with our predictions, we observed significant interspecific differences in daytime microhabitat use: species that had both placentation and superfetation were found in deeper and faster-flowing parts of the river, species that lacked both adaptations were confined to shallow slow-flowing areas, and species with one adaptation (i.e. only superfetation) inhabited intermediate areas. This interspecific daytime microhabitat use was strongest in reproductive adults, intermediate in immatures, and absent in juveniles (the latter of which were all found in shallow low-velocity zones), suggesting that ontogeny influences species-specific microhabitat use. Finally, at night, all fishes, regardless of the species or age-class, congregated in shallow slow-flowing waters to rest (sleep) on the river bottom. Taken together, our results suggest that placentation and superfetation may be hitherto unrecognised reproductive features that help to explain differences in ontogenetic and diurnal microhabitat preferences between sympatric live-bearing fish species living in environments characterised by large flow variation.