Ecological restoration of eutrophic lakes using aquatic macrophytes is an important and practical technology. Here, we investigated the response of phytoplankton and zooplankton to a large-scale 2015-built aquatic macrophyte enclosure (AME, 200,000 m²) screened of by a PVC net in Baima Lake, a eutrophic lake, from spring to autumn of 2019. AME significantly improved water quality by increasing water transparency, and reducing total nitrogen, total phosphorus, and chlorophyll-a content during the growing season. AME significantly decreased phytoplankton abundance and biomass and marginally increased zooplankton abundance and biomass. Phytoplankton and zooplankton communities were closely related to environmental factors, such as water temperature, conductivity, total phosphorus, chemical oxygen demand, and chlorophyll-a inside and outside the AME. The zooplankton:phytoplankton biomass ratio inside was slightly higher than outside the AME. Zooplankton and phytoplankton biomass were significantly positively correlated inside and outside the AME, as were chlorophyll-a and total phosphorus. We found phosphorus to be a key factor limiting primary productivity in Baima Lake, and that bottom-up effects were the main driver to control phytoplankton in the AME. Using aquatic macrophytes to reduce nutrient loads is an effective way to manage eutrophication in Baima Lake.