Gyrodactylids are ubiquitous fish parasites and yet, with the notable exception of Gyrodactylus salaris, few studies have reported the effect of these parasites on host survival in natural populations. Here, we assess the impact of the parasite load of gyrodactylids (G. turnbulli and G. bullatarudis) on the survival and migration of guppies (Poecilia reticulata) in their natural habitat of the Aripo River in Trinidad. The recapture rate of males declined by 19% with every additional parasite, a remarkably high figure given that the parasite load in this study ranged from zero to 20 worms. In addition, with an increased number of parasites, males were more prone to be recovered downstream. In contrast, no effect of parasitism was observed in females. The mean parasite load sharply declined after a series of flushing events during heavy seasonal downpours. The parasite load varied significantly between fish depending on their location in the river, and the size of the fish explained variation in parasite load between individuals. The present study indicates that tropical gyrodactylid parasites can play an important role in the ecology of natural fish populations, causing intense bouts of natural selection in guppies during heavy rains in the wet season.