Abstract Parasitism rates can vary dramatically across large and small spatial scales. Such heterogeneity in infection is driven by variation in environmental factors that influence the probability of host and parasite encountering each other (encounter filters) and of genetic and physiological factors that alter whether that encounter results in a successful infection (compatibility filters). Here, we investigated how infection in first‐intermediate hosts (snails) by trematode parasites is influenced by small‐scale variation in environmental variables (final host relative abundance, nutrients, and temperature) and population origin across multiple ponds within an artificial flow‐through wetland system in Atlanta, GA, U.S.A. We placed individually marked, lab‐reared F1 generation snails of the same age from three different populations into field enclosures at nine ponds along a 1‐km stretch of connected, flow‐through ponds for 86 days and allowed them to accrue infections naturally. This highly controlled field experiment allowed us to disentangle the underlying factors influencing small‐scale variation in infection risk, which can be masked when looking only at natural patterns of infection prevalence across space. We found high heterogeneity in infection risk. The probability of infection was highest in ponds downstream and with high levels of bird activity; population origin was not important. This work provides experimental evidence that infection risk varies across small spatial scales (tens of metres), driven by steep gradients in influential environmental drivers, emphasising the importance of controlled field manipulations to understand infection risk. Identifying small‐scale drivers of infection risk can help mitigate infection in hosts of interest (e.g., humans, fish), and should be acknowledged in organismal field studies, where infection and infection risk may influence the ecology, physiology, or behaviour of animals.