Tropical riparian forest species differ in their seasonal and inter-annual production of litter that alters the habitat quality of shallow headwater pools. Future “flash drought” (rapid onset, variable duration) and “persistent drought” (slow onset, long duration) conditions are likely to occur more frequently in the Caribbean and cause “hydrological drought” as well as affect the timing and amounts of riparian litter production. Relative short periods of higher temperatures increase evapotranspiration and decrease soil moisture that can synchronize increased litter fall among riparian tree species. These pulsed litter inputs coupled with decreased flow regimes initially create high food availability for freshwater decapods along with protective cover in pools with accumulated litter. These high-quality habitats can lead to periods of increased population densities of shrimp and crab detritivores. However, prolonged dry periods with low or no flow result in poor habitats characterized by low dissolved oxygen, warmer water temperatures, low pH, with high tannin- and other litter-leachate concentrations. Consequently, some decapods move within a contracted drainage network in search of higher-quality pools (deeper, groundwater-fed, cooler, riparian shaded, interconnected) where sustainable amounts of litter remain available. These pools undergo increasing population densities and can result in competition for feeding territories among adult shrimp. Long-term data indicate that the movement of Macrobrachium carcinus and Macrobrachium crenulatum to and from the uppermost headwater pools can be an expected response as future droughts occur in the Quebrada Prieta drainage of the Luquillo Experimental Forest in Puerto Rico. These changes can shift future population dynamics of these co-occurring migratory species that have life cycles dependent on access to both estuaries and upstream habitats where distances of larval transport and post-larval upstream migrations affect population recruitment.