1. Understanding how changes in hydrological regime and intrinsic host factors drive parasite loads and dynamics remains a challenging issue in aquatic parasitology. Many host-parasite systems have shown that host-related factors can influence parasitism in freshwater systems. Temporal changes in the hydrological regime are also one key factor that could alter the streamflow and habitat area and indirectly affect the interactions between ectoparasite and host. However, there are still few studies on the combined effects of both streamflow regime and intrinsic host factors to investigate variations in parasite loads on stream ecosystems. 2. Here, we used a cymothoid-palaemonid prawn model to test whether host-related traits and the temporal changes in streamflow and area caused by the rainfall regime could influence ectoparasite loads in stream habitats. Prawns were collected seasonally over 4 years in a tropical stream in southeast Brazil. We also tested the hypothesis of whether the prawn body size covaries with cymothoid body size, and also whether this change between sex and seasons. 3. We found a strong relationship between the ectoparasite and host body sizes, which confirms Harrison’s rule of this host-ectoparasite system. Our best model showed an effect of host body size, host sex, and host molt stage, but not host age, on ectoparasite loads. Prawn females have higher ectoparasite loads than males, and there was a positive association with the ecdysis stage. Our model also predicts that decreased rainfall could increase parasitism in dry seasons by reducing the natural flow regime and habitat area in these tropical stream systems. 4. Our findings show that temporal variability in streamflow is a key environmental factor combined with host-related characteristics to drive the parasite dynamics of a cymothoid-prawn system in stream habitats.5. Identifying how the interactions between aquatic invertebrates and parasites respond to the variability in hydrological conditions can help to understand how infections and parasitism may affect the benthic invertebrates play in stream systems.