Few studies have explored the relationship between benthic and planktonic assemblages in reservoirs, despite their role in food chains and maintaining ecological functions. Macroinvertebrates play a crucial role in food webs and contribute about 42% of whole-lake secondary productivity. Therefore, their status is vital for maintaining good ecological functions. In this study, we selected Nanwan Reservoir, a eutrophic thermally stratified reservoir in China, to evaluate the community of macroinvertebrates in different seasons and explore the relationships between macroinvertebrate assemblages and different planktonic groups, including phytoplankton, protozoans, rotifers, and planktonic crustaceans. Cyanophyta and Bacillariophyta dominated the phytoplankton assemblages, and their proportions varied with seasons. The bad community of macroinvertebrates in summer, autumn, and winter could be attributed to the excessive growth of Cyanophyta or other phytoplankton. Based on the results of partial least squares regression, an algorithm used for prediction, we determined that the excessive growth of algae, crustaceans, protozoans, and Cyanophyta was detrimental to the development of macroinvertebrates, and was indicative of high nutrient loads in the reservoir. However, the growth of Bacillariophyta, Chrysophyta, and Euglenophyta was advantageous to macroinvertebrate assemblages and indicated a better ecological condition of the reservoir. The results of partial least squares structural equation modeling demonstrated close associations between phytoplankton and both zooplankton and macroinvertebrates, indicating their interdependence in this reservoir system. Our study results imply that the status of macroinvertebrates can be predicted by the abundance of some planktonic assemblages, and cost savings from selecting one of the planktonic groups to monitor ecological conditions could be accomplished in future studies.