Throughout the humid tropics, increased land disturbance and concomitant road construction increases erosion and sediment delivery to rivers. Building road networks in developing countries is commonly a priority for international development funding based on anticipated socio-economic benefits. Yet the resulting erosion from roads, which recent studies have shown result in at least ten-fold increases in erosion rates, is not fully accounted for. While effects of road-derived sediment on aquatic ecosystems have been documented in temperate climates, little has been published on the effects of road-induced sediment on aquatic ecosystems in developing countries of the tropics. We studied periphyton biomass and macroinvertebrate communities on the deltas of Río San Juan tributaries, comparing north-bank tributaries draining undisturbed rain forest with south-bank tributaries receiving runoff from a partially-built road experiencing rapid erosion. Periphyton biomass, richness and abundance of macroinvertebrates overall, and richness and abundance of Ephemeroptera, Plecoptera and Trichoptera were higher on the north-bank tributary deltas than the south-bank tributary deltas. These findings were consistent with prior studies in temperate climates showing detrimental effects of road-derived fine sediment on aquatic organisms. A Non-Metric Multidimensional Scaling (NMDS) analysis showed the impacted community on the south-bank deltas was influenced by poorly-sorted substrate with greater proportions of fine sediment and higher water temperatures.