Host heterogeneity can impact parasite transmission, but determining underlying traits and incorporating them into transmission models remains challenging. Body size is easily measured and influences numerous ecological interactions, including transmission. In the snail-schistosome system, larger snails have a higher exposure to parasites but lower susceptibility to infection per parasite. We quantified the impact of size-based heterogeneity on population-level transmission by conducting transmission trials in differently size-structured snail populations and competing size-dependent transmission models. Populations with greater proportions of large snails had lower prevalence, and small snails were shielded from infection by co-occurring large conspecifics. Using the winning size-explicit model, we then estimated that schistosome transmission potential varies dramatically across time due to seasonal changes in snail population size structure. Thus, incorporating traits such as body size, which are impacted by and directly affect host ecology, into transmission models could yield insights for natural dynamics and disease mitigation in many systems.