In nowadays, world trade and cargo transportation mainly rely on shipping, and inland ports provide valuable and essential services to the maritime transport. With the increase of trade volume, the discharge of ballast water from ships is also increasing, which brings in ecological challenges. The International Maritime Organization stipulates that the number of organisms in discharged ballast water should be limited to prevent biological invasion to recipient waters. However, ballast water still contains many substances of source water, and may affect the plankton community in the recipient waters. In this study, the effects of ballast water on nature freshwater plankton community were evaluated at laboratory scale. It was observed that the abundance and diversity of planktons decreased with increase of water salinity. Through 10 days of continuous monitoring, it was found that ≥ 50 µm organisms were more sensitive to rising salinity than 10–50 um organisms, when water salinity was not over 3.6‰, there was no significant difference on ≥ 50 µm organisms quantity and diversity compared with the freshwater control group after 10 days, and the biota maintained certain recovery ability, while 10–50 um organisms had recovery ability when water salinity was not over 6.5‰. However, when the water salinity was over 6.5‰, both species composition and organism density showed irreversible and rapid reduction. In addition, organism species Platyias sp., Polyarthra sp., Tribonema sp., Navicula sp. were found to be very sensitive to salinity change and could be considered as indicative organisms for monitoring and evaluating ecological effect of discharge of saline ballast water. This is of great significance for the scientific management of ballast water discharge in fresh waters in the future.