As climate change continues to alter precipitation regimes over the tropics, many stream ecosystems are experiencing frequent periods of low flow and drought. We designed a flow reduction experiment to assess the effects of low-flow conditions on stream fauna and ecosystem processes in Puerto Rico. Our study was conducted within the Luquillo LTER research program at the Luquillo Experimental Forest, Puerto Rico. Here, our goal was to explore the response of stream macroinvertebrates to recurrent low-flow conditions. We used a pair of small headwater streams, manipulated flow in one, and used the other as a reference. Following climate model predictions, flow was reduced from March to July (the less rainy months) for two consecutive years. We monitored benthic macroinvertebrates, aquatic insect emergence, and freshwater shrimp monthly. The flow reduction was effective in maintaining our experimental stream in low flow conditions, but large floods affected both streams. Insect assemblage composition and structure reflected changes in flow, but appear to be mostly controlled by the presence of shrimp. Shrimp assemblages were stable over time and did not appear affected by low or high flow. Overall, macroinvertebrates (insects and shrimp) in our studied rainforest streams can cope with the low flow as long as conditions stay within the natural variability of the system and dissolved oxygen is not depleted.