Stream-dwelling benthic macroinvertebrate taxa associate to preferred habitats, but research defining these associations is sparse for many areas of Central America, especially under pristine ecological conditions. We explored patterns of benthic macroinvertebrate community structure among mesohabitats and substrate conditions within 8 headwater streams in the Indio-Maíz Biological Reserve, a protected lowland broadleaf rainforest in southeastern Nicaragua. Among 92 genera, 24 were identified as indicators of mesohabitat types. Riffles and rapids each harbored nearly twice as much biodiversity as pools did. However, rapids supported the highest number by far of indicator taxa associated with a single habitat, and community ordination further affirmed that rapid communities were the most distinctive among mesohabitats. Collector–gatherers constituted >50% of all individuals among functional feeding groups, and riffles harbored the greatest functional feeding group evenness among mesohabitats. Despite a paucity of shredders in these communities, multiple taxa (n = 9) were indicators of leaf cover. These results highlight the value of distinguishing mesohabitats beyond a pool–riffle dichotomy because rapids with maximal fast flows and minimal embeddedness likely provide critical well-aerated and structurally complex refugia in warmwater tropical streams. Minimally embedded habitat patches with abundant leaf cover appear to be especially important for supporting macroinvertebrate biodiversity. Given that study sites drained watersheds with fully intact tracts of primary rainforests, our results likely reflect reference conditions for benthic macroinvertebrate communities in lowland Central American streams. Descriptions of macroinvertebrate habitat affinities from pristine settings, such those presented here, can help inform biomonitoring and conservation efforts in a region with rapidly degrading aquatic ecosystems driven by land-use change.