Our understanding of the drivers of parasite community structure is compromised by poor sampling and historical focus on one host-one parasite systems. Yet parasites are ubiquitous and co-infections are common. This study aimed to identify how a range of drivers (connectivity, region, host-parasite interactions, parasite-parasite interactions) contribute to structuring endoparasite metacommunities. Within-host to landscape level patterns of malacosporean myxozoans infecting dormant propagules (statoblasts) of the freshwater bryozoan, Cristatella mucedo, were characterised. Large-scale databases were used to develop a metric for waterbird connectivity based on species turnover. Overall infection prevalence, assessed by PCR, was associated with high waterbird turnover at the site level, providing evidence that waterbirds act as parasite dispersal vectors. RFLP analysis revealed eight malacosporean infection profiles. Traits of both hosts (e.g. habitat preferences) and parasites (e.g. transmission success) were linked with impacts of hydrological connectivity. Flooding regimes, nutrient enrichment from agriculture landscapes, and waterbird abundance were linked with regional impacts. Co-infections within tiny statoblasts (up to four) were common. Uninfected statoblasts were larger and there was no detectable difference in sizes of statoblasts with single vs. multiple infections. Co-occurrence analysis identified positive associations between four malacosporean taxa. The lack of negative associations suggests no competition amongst malacosporeans infecting statoblasts. There was no evidence that host-parasite interactions result in local adaptation of parasites to host clones. Hydrologically isolated sites had greater malacosporean diversity and enhanced levels of overall infection prevalence and co-infection, suggesting that such sites are malacosporean hotspots. Our study provides novel insights on the complex factors that can structure parasite communities in freshwater invertebrate hosts across the UK.