The aim of the present study was to identify the parasite fauna of cultured rainbow trout (Oncorhynchus mykiss Walbaum, 1792) and Arctic charr (Salvelinus alpinus (L.)) from a flow-through aquaculture system at Lake Tollense in northern Germany.The fish were sampled during different seasons in 2018 from an open freshwater raceway. For rainbow trout, 10 different parasite species were isolated, belonging to Monogenea (1), Cestoda (2), Crustacea (2) and Digenea (5), including the eye flukes Tylodelphys clavata Niewiadomska, 1984, Diplostomum pseudospathaceum and Diplostomum spathaceum (Rudolphi, 1819) Olsson, 1876, the latter representing a potential pathogenic species, which was molecularly identified and reported as a core species with prevalences of 80.0%-100.0% and high mean abundances of 42.8-55.0. Arctic charr only harboured T. clavata and D. spathaceum. Other taxa were found with low prevalence in the summer season exclusively, indicating strong seasonality of the detected parasites. Statistical correlation was positively tested for coherences of eye fluke burden and fish growth, weight and performance between seasons, recommending implementation of an enhanced aquaculture management for the surface waterdependent flow-through aquaculture system at Lake Tollense.