Despite the consumption of disinfectants have been increased by COVID-19 pandemic, the fate of the chemicals in aquatic food webs are still unclear. In order to understand the trophic transfer of the chemicals, the concentration of disinfectants including six benzalkonium chloride (BACs) and five didecyldimethylammonium chlorides (DDACs) were measured at the Geum (2020), Han (2021), and Yeongsan River (2021), before and after rainfall. The highest concentration of ΣBACs (mainly C12 and C14) and ΣDDACs (mainly C10 and C14) were observed in the Han River, followed by Yeongsan River, Geum River Estuary, and Gapcheon. After rainfalls, both concentration and detection frequency were decreased in all sites. Although the BAC and DDAC seems to be accumulated in organisms, they were bio-diluted rather than magnified in the aquatic food web with the biomagnification factor (BMF) of less than 1, trophic magnification slope (TMS) from - 0.236 to 0.001, and trophic magnification factor (TMF) from 0.85 to 1.01.