Coastal zones support the most productive marine ecosystems, yet they are increasingly threatened by anthropogenic stressors such as dredging. In this study, we investigated how seasonal variation and dredging activities conducted during the construction of a harbor and submarine base (Sepetiba Bay, RJ, Brazil) affected the phytoplankton and zooplankton assemblages. The observed temporal variability at five different sites over 10 years revealed that dredging exceeds the expected influence of dry and rainy seasons on plankton abundance and diversity. In general, the abundance of both groups increased during dredging due to the resuspension of nutrients and benthic organisms. This increase was particularly evident in the dinoflagellate Scrippsiellaa cuminata, the diatoms Thalassiosira rotula and Nitzschia longissima, and the herbivorous zooplankton Acartia clausii and Pseudevadne tergestina. Moreover, season and dredging activities synergistically influenced plankton assemblages, resulting in larger seasonal variations during dredging activities. After the end of the harbor construction, plankton abundance decreased and remained low until the end of the monitoring, which may indicate persistent changes in the biodiversity and ecosystem functioning of impacted areas.