This work aims to assess the main factors that determined the variability of environmental and biological variables in wastewater reservoirs of the Right-Bank Sorbulak Canal system (South-Eastern Kazakhstan). We used standard methods for the collection and analysis of data, as well as the principal components analysis (PCA) to assess the relationship between environmental and biological indicators. The average depth of the surveyed reservoirs was 4.1–10.0 m, temperature—21.7–25.7 °C, pH—9.41–10.00, permanganate index—16.22–19.07 mgO/dm3, N-NO2—0.03–0.13, N-NO3—1.28–3.00, N-NH4—0.30–0.53, PO4—0.14–0.39, Si—3.69–8.26, Mn—0.03–0.07, Fe—0.34–0.38 mg/dm3. The content of Cd, Co, Pb, Zn, and Cr was low, Cu—0.012–0.036 mg/dm3. The water quality is influenced by the wastewater composition, chemical interactions, morphometric and physical-chemical conditions of the reservoir, pollution of the coastal area, and secondary water pollution. Changes in the species composition and zooplankton abundance reflected the instability of external conditions. PCA showed the priority influence of carbonates, bicarbonates, magnesium, temperature, nutrients, and heavy metals on zooplankton structure. The results obtained demonstrate the indicator significance of zooplankton, and the methodological approaches can be used to assess water bodies with the complex pollution located in other regions.