P>1. Overlapping river and road networks provide a framework for studying the complex interactions between natural and human systems, with river-road intersections as focal areas of study. Roads can alter the morphology of stream channels, pose barriers to freshwater fauna, provide easy access to streams for humans and non-native species and accelerate the expansion of urban development. 2. We determined what variables control the structure of diadromous fish and shrimp communities and assessed whether particular road crossings altered community structure in north-eastern Puerto Rico. We identified 24 sites that represented a range of river and road sizes across two catchments that drain El Yunque National Forest in Puerto Rico. 3. The location of natural barriers and the size of stream pools were the most important variables for predicting six of fifteen fish and shrimp distributions. Predatory fishes were predicted to be limited to areas in the river network below large, steep waterfalls, whereas adult shrimp Atya lanipes (Atyidae) were predicted to be present above these waterfalls. The fish Awaous banana was predicted to be present in pools > 11.6 m wide, whereas the shrimp Xiphocaris elongata was predicted to be present in pools < 10.4 m wide. The distributions of nine species were predicted poorly, but three of these species were common and three were rare. 4. Although urban and agricultural land covers were among the top three predictors of five species distributions, they were probably good predictors because they were correlated with the natural gradient. Further study is necessary to disentangle natural and anthropogenic gradients. 5. Road crossings, 10 of which were culverts, were not dispersal barriers for fishes or shrimps. On average, species were present both upstream and downstream from road crossings at 68% of sites where they occurred. Absences upstream or downstream from road crossings occurred at 16% of sites each and likely resulted from a failure to detect species. 6. Several existing features of these catchments and taxa may aid in fish and shrimp conservation. The headwaters are protected by management practices of El Yunque National Forest, connectivity within the river network has been maintained, and the diadromous life history of these organisms makes them resilient to pulsed disturbances.
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