The National Ecological Observatory Network (NEON) is a continental-scale network of monitoring sites which collect long-term, open-access data to better understand ecological change. NEON includes two neotropical freshwater streams in Puerto Rico, the Rio Cupeyes and Rio Yahuecas. Like all NEON sites, they are instrumented with an array of in-situ sensors which collect high-frequency measurements including rainfall, streamflow, temperature, and water quality. Observational sampling of aquatic plants, macroinvertebrates and fish are conducted seasonally 2-3 times per year. The two sites were selected to span a gradient of ecoclimatic variables, providing a contrast not only with temperate NEON sites located in the continental Unites States, but with each other. Both sites are second-order streams (watershed area 4.3 and 9.5 km2 respectively) in the Cordillera Central. The most noticeable difference between the sites is the degree of riparian shading, with Rio Cupeyes having a nearly fully enclosed canopy, while Rio Yahuecas is much more open. These differences in light availability affect rates of primary production and community structure across the two streams. In contrast with more temperate streams however, both sites exhibit a much smaller degree of seasonal variation. It is estimated that around 2/3 of global streamflow originates in the tropics, yet tropical streams remain critically understudied. Data from these sites complement the other NEON sites, include taxa typically not found on the mainland, and provide a more complete understanding of ecological drivers across continental scales.