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The outbreak of COVID-19 led to the extensive use of disinfectants in urban areas. These disinfectants, along with disinfection by-products (DBPs), eventually enter waters and affected the aquatic organisms. But little information could be obtained on disinfectants threatening aquatic ecosystems. This study was conducted to obtain insight into the effects of massive use of disinfectants on freshwater ecosystems, DBPs, phytoplankton, and zooplankton in nine urban and two country lakes in Wuhan during the COVID-19 pandemic; in addition, the residual chlorine in the South Lake (one of the urban lakes), was investigated. The concentration of residual chlorine in the South Lake ranged from 0.000 mg L−1 to 0.427mg L−1, with an average concentration of 0.092 mg L−1. The total concentrations of DBPs (halogenated aliphatic DBPs and aromatic halogenated DBPs) detected in the urban and country lakes ranged from 4.22 μg L−1 to 16.59 μg L−1 and 5.92 μg L−1 to 7.84 μg L−1, respectively. There was no significant difference in DBPs content between urban lakes and country lakes (p < 0.05). Mann–Whitney U tests showed no significant differences in plankton cell density, biomass, and alpha diversity indexes between urban and country lakes, except for the Shannon−Wiener diversity index of phytoplankton. Beta diversity demonstrated that plankton communities at different sampling stations in urban and country lakes were not significantly separated into two groups, but rather intersected each other. Variance partitioning analysis revealed that the composition of plankton communities was primarily influenced by other plankton organisms and community stability under the conditions of the investigated factors. Results indicated that the detected plankton communities in urban lakes from Wuhan were not significantly affected by the use of disinfectants. It could be deduced that the massive use of disinfectants in this outbreak had no significant impact on the plankton communities. [ABSTRACT FROM AUTHOR]