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Most of the human population lives in cities, and understanding their impact on freshwater environments is essential. Streams in cities face many environmental challenges that have been described in the concept of Urban Stream Syndrome. This concept illustrates urban streams’ biological, hydrological, chemical, and physical stressors. In tropical streams, these stressors impact shrimp, fish, insects, and other macroinvertebrates that inhabit the freshwater ecosystems. Freshwater shrimp are vulnerable to urban activities, physical, chemical, and ecological impacts. For this reason, these organisms have been used as biological indicators of stream health in the tropics. The shredder shrimp Xiphocaris elongata plays a fundamental role in the organic matter process and decomposition. The objectives of this study were to characterize the population of X. elongata and to identify differences in the abundance of X. elongata between urban and forest streams. Our results showed that highly urbanized areas have a significantly lower abundance of the shredder shrimp X. elongata than medium or low urban reach in the urban and forested watersheds. This study also showed that physicochemical and geomorphological variables are important environmental factors that influence the abundance of X. elongata in Puerto Rican streams.