The present investigation examines how the environmental factors and phytoplankton functional group structure influence the zooplankton community in Lake Kuriftu, an important ecological indicator for water quality assessment. Biological and physicochemical data samples were collected monthly from December 2020 to April 2021. Zooplanktons were identified using an inverted microscope at different magnifications. Concentrations of NO3-N, NH3 + NH 4 + -N, total phosphorous (TP), and soluble reactive phosphate (SRP) ranged from 21.905 to 25.81, 48.52 to 57.095, 64.201 to 83.60, and 22 to 34.867 µg L−1, respectively, while molybdate-reactive silica ranged from 6.297 to 9.33 mg L−1. Physicochemical analyses indicated that Lake Kuriftu is turbid, shallow, and exhibits eutrophication, with elevated nutrient levels and alkaline conditions. Twenty-six zooplankton taxa were recorded, including 5 Cladocera, 7 Copepoda, and 14 Rotifera. Rotifers were the most dominant group, followed by copepods. Redundancy analysis (RDA) identified SiO2, TP, Secchi depth (ZSD), total nitrogen (TN), and salinity as the main factors influencing interactions between zooplankton and phytoplankton functional groups. TP, ZSD, and salinity exerted negative effects, while SiO2, TN, and zooplankton species such as Polyarthra and Keratella had strongly positive influences. Functional groups (FGs) SN, F, and N were positively and strongly affected by TN and by Polyarthra and Keratella, while N correlated positively with Secchi depth (ZSD). These results demonstrate that nitrogen pollution is a primary driver of the lake’s trophic structure, advancing its eutrophic state. Immediate nutrient management strategies are essential to prevent further degradation of Lake Kuriftu water quality.