The Caribbean region is experiencing increasingly frequent periods of low precipitation, resulting in recurrent low-flow conditions in streams. According to climate models, these conditions will become more common in the future. Low flow could favor biotic interactions. Here we studied the effects of low flow conditions on the top-down control that shrimp have on benthic communities. Shrimps are major macroconsumers in tropical island stream ecosystems. Specifically, we assessed the effects of shrimp foraging activities on macroinvertebrate assemblage composition and structure and whether those effects are altered under low flow conditions. Our study site was Quebrada Prieta, in El Yunque National Forest, Puerto Rico. Prieta has two tributaries, one remains with its natural flow and the other has an experimental flow reduction. This study is part of the long-term StreamFRE project which reduces flow by 40%. We selected four pools in each tributary and ran an electric exclusion experiment. Each pool had one quadrat to exclude shrimp and one as a control quadrat. Overall, we had two flow treatments (natural and reduced) and two shrimp treatments (exclusion and control). After 25 days of shrimp manipulation, we measured macroinvertebrate abundance and measured benthic chlorophyll concentration and organic matter. Shrimp exclusion effects were different in the natural flow vs. low flow stream. In the natural flow stream, we did not find significant effects of shrimp exclusion. However, we found large pool-to-pool variation in macroinvertebrates. In the low-flow stream, shrimp had a strong top-down control over macroinvertebrates. Overall, our study supports previous studies that indicate that shrimp play a major role in controlling benthic resources and invertebrates in tropical island streams. However, we found that those controls are much stronger under low flow conditions. Given climate projections for the Caribbean, our findings suggest that biotic interactions could become stronger.