The crustacean zooplankton in Lake Biwa play a vital role in the lake's food web and maintain the lake environment. Epibionts impact the biology and ecology of host zooplankton, and its biological implications may play an important role in the lake ecosystem. In this study, we reported the episymbiotic infection on cyclopoid copepods during the stagnation period of 2018-2022 in Lake Biwa. Zooplankton samples were collected monthly with a vertical net haul from the bottom to the surface at a pelagic site of Lake Biwa from January 2018 to December 2022. At the same time, temperature, dissolved oxygen, and Chlorophyll-a were measured throughout the water column. Crustacean zooplankton species and episymbionts were identified and counted. This study focused on the relationship between episymbionts and their host, i.e., cyclopoids, and investigated the morphological characteristics and identification of the episymbionts, as well as year-to-year and seasonal variations in their infection rates on cyclopoids. Two epibiont species were identified, i.e., epizoic flagellate Colacium vesiculosum, and peritrich ciliate Epistylis anastatica. No such infection was found in other crustacean zooplankton, including the most dominant Eodiaptomus japonicus and Daphnia spp. Lake water was stratified from June to October each year. And an oxygen-minimum layer was formed just below the thermocline from July, just after the massive phytoplankton bloom in June, to September. Episymbiotic infestation was generally found from May to December each year, but not from January to April. The infestation prevalences were high from August to November. The infestation prevalence was positively correlated with temperature or host abundance, and negatively correlated with dissolved oxygen. The minimum oxygen-containing water layer might be associated with microbial activity in depositing organic material from phytoplankton blooms. Epizoic ciliates such as Epistylis mainly feed on microbial components, including free-living bacteria and detritus, while flagellate Colacium may use dissolved organic carbon (DOC). The stratified lake water in early summer each year may therefore induce favorable conditions around the thermocline for epiphytic ciliates and flagellates through the microbial food chain.