Urbanization is one of the major threats to stream ecosystems worldwide. The phrase “urban stream syndrome” has been coined to describe patterns in degraded streams draining urban land. In Puerto Rico, urbanization now covers 16% of the island. The fully protected Luquillo Experimental Forest (focus of the LUQ-LTER) is only 23 km from the center of San Juan, a city of 1.3 million. Therefore, LUQ is assessing the impacts of urbanization on tropical stream ecosystem structure and function. This understanding will expand our knowledge of forested streams in the Luquillo Mountains. We focus our studies on the Rio Piedras watershed, which drains the San Juan Metropolitan Area. However, we are also studying other less urbanized systems in Puerto Rico. Urban stream ecosystems showed the expected responses to urbanization with respect to nutrient loads and macroinvertebrates. Highly urbanized streams had high levels of phosphate and ammonium and macroinvertebrate assemblages dominated by tolerant taxa (e.g., snails, Chironomidae). Other factors, however, did not follow expected responses to urbanization. Stream hydrology appears to be equally flashy in streams draining forested and urbanized watersheds. Fish assemblage integrity was not degraded in response to urbanization and all native fish species were found in the highly urbanized Rio Piedras watershed. River connectivity appears to be more important than urbanization in determining fish assemblage composition in Puerto Rican streams. As urbanization continues to increase in Puerto Rico, studies by the LUQ LTER will provide critical information on human impacts to streams.