Next generation sequencing (NGS) technologies are extensively used to dissect molecular mechanisms of host-parasite interactions in human pathogens. In contrast, the power of NGS is yet to be fully realizedin ecology as a rich source for formulating and testing new hypotheses. Here, we studied Eurasian perch (Perca fluviatillis) and its eye parasite (Diplostomidae) communities in fourteen lakes that differed in humic contentto test host-parasite-environment interaction. We hypothesised that high humic content would decrease pH and the abundance of the intermediate hosts (gastropods), potentially changing Diplostomidae community structure and potentially affecting perch host immune response. This hypothesis was invoked by RNA-seq data and later cross-validated with PCR-based and extensive metabarcoding approaches. The results demonstrate how humic acid-related changes in the extrinsic environment may shape common parasite communities and host immune response. This study also highlights the utility of integrating RNA-seq and metabarcoding approaches in host-parasite community studies.