The eutrophication of three small lakes in the aquatic zones at the Huainan coal mine subsidence areas, designated as east site (ES), central site (CS), and west site (WS), were studied. Nutrient content, species, and nitrogen (N) to phosphorus (P) ratios were obtained through water quality analyses. Nutrient limitation was evaluated by nutrient enrichment bioassays (NEBs) in the autumn of 2012 and spring of 2013. Average annual concentrations of total phosphorus (TP) were 0.05, 0.08, and 0.10 mg/L, and total nitrogen (TN) concentrations were 0.77, 1.95, and 2.06 mg/L in the water column at CS, ES, and WS, respectively. All of the three lakes exhibited ‘meso-eutrophic’ states and the TN:TP ratio ranged from 25:1 to 74:1 with variability between seasons and sites. NEBs verified that primary productivity in the lakes at ES and WS were mainly limited by P, while N limitation or N and P co-limitation was present in the aquatic zones at CS due to unavailable dissolved inorganic nitrogen. In the studied lakes, the blue-green algae, which comprised 70% of all identified species, was the predominant taxa, while the micro-zooplankton taxa was dominant, indicating a typical trophic structure of eutrophic lakes.