Physical habitat structure can influence the distribution and abundance of organisms. In rivers, stream drift, a common process originating from the unidirectional water flow, favours the displacement and downstream dispersion of invertebrates. This process could also generate a gradient in infection levels, leading to decreasing numbers of parasites per host as one moves upstream from the river mouth. We tested this hypothesis using 4 trematode species infecting the fish Gobiomorphus breviceps in the Manuherikia River (New Zealand). We analysed the abundance of each trematode infrapopulation as a function of distance from the river junction and fish size by generalized linear models. Our results supported the existence of a longitudinal gradient in trematode abundance along the river with a decreasing downstream-to-upstream continuum. This applied to 3 out of the 4 trematode species studied, suggesting that this might be a common pattern in river populations. Thus, the unidirectional river flow and a major process like drift in lotic systems, that influences the dynamics and distribution of invertebrate hosts, can also affect trematodes. Host properties like habitat preference, and parasite traits, particularly those related to transmission mode can influence the strength of the observed gradient, as may other environmental and biotic factors.