Semi-aquatic European water frogs (Pelophylaxspp.) harbour rich helminth infra-communities, whose effects on host population size in nature are poorly known. To study top-down and bottom-up effects, we conducted calling male water frog counts and parasitological investigations of helminths in waterbodies from different regions of Latvia, supplemented by descriptions of waterbody features and surrounding land use data. We performed a series of generalized linear model and zero-inflated negative binomial regressions to determine the best predictors for frog relative population size and helminth infra-communities. The highest-ranked (by Akaike information criterion correction, AICc) model explaining the water frog population size contained only waterbody variables, followed by the model containing only land use within 500 m, while the model containing helminth predictors had the lowest rank. Regarding helminth infection responses, the relative importance of the water frog population size varied from being non-significant (abundances of larval plagiorchiids and nematodes) to having a similar weight to waterbody features (abundances of larval diplostomids). In abundances of adult plagiorchiids and nematodes the best predictor was the host specimen size. Environmental factors had both direct effects from the habitat features (e.g., waterbody characteristics on frogs and diplostomids) and indirect effects through parasite-host interactions (impacts of anthropogenic habitats on frogs and helminths). Our study suggests the presence of synergy between top-down and bottom-up effects in the water frog–helminth system that creates a mutual dependence of frog and helminth population sizes and helps to balance helminth infections at a level that does not cause over-exploitation of the host resource.