Urban expansion has become a globally dominant process. Urban sprawl (excessive spatial growth or expansion around cities) as defined by Brueckner (2000), has resulted in a wide range of impacts on ecosystems. One of the most significant effects of urbanization on streams is the altered geomorphology consequently resulting in many important changes to ecological processes, biodiversity, and stream function (Bencala, 2000; Gücker & Boëchat, 2004; Fisher et al., 2007; Hamilton et al., 2007). The purpose of this study was to determine the nitrate retention rates in urban tropical streams with varying geomorphology. Another objective of this study was to see the seasonal patterns of N cycling, and if channel heterogeneity acted as a buffer. The study took place at three streams from the Río Piedras watershed, located at the highly urbanized city of San Juan in the tropical island of Puerto Rico. We performed six short-term nitrate injections (30-80 min) in different days at each of the three streams (i.e. stream with natural geomorphic features, intermediate, and channelized) in order to assess N uptake during varied weather conditions. Then we calculated nitrate uptake length (Sw), uptake velocity (Vf), and uptake rate (U). Interestingly we obtained high N retention rates in all streams. Also, unpredicted short uptake lengths and high uptake rates were obtained in the channelized stream, which may be related to intensive N cycling in the benthic biofilm. Seasonal changes of weather conditions also influenced N retention capacity regardless of geomorphic features. However, as expected water temperature, specific conductance, and NO3 − concentration were significantly lower in the geomorphologically complex stream than in the intermediate and channelized streams. In addition, urban tropical streams may follow a Michaelis-Menten saturation response due to the high N loads. We conclude that N uptake is a continuing vital ecosystem function in urban watersheds even at high NO3 − concentrations, which reduces N export. We also learned that benthic biofilm may be one key control of N retention in highly impacted urban tropical streams. Therefore, this study confirms the need for stream conservation efforts, specifically the reduction of N loading in order to prevent eutrophication of coastal ecosystems.