A 70-day experiment was carried out to estimate mathematical equations that describe the effect of water quality and nutrient input on different zooplankton community count under biofloc conditions. The experiment was designed to deliver three diets with different dietary C/N ratios (8.8, 11.5 & 12) by manipulating the dietary protein (CP) and/or dietary lipid (L). The three diets were; control diet (C; 30% CP, 8% L), P₂₃L₈ diet (23% CP, % 8 L) and P₂₃L₁₀ diet (23% CP, 10% L). Control was the only treatment supplemented with an external carbon source (starch) to reach a C:N ratio of 10:1. The control treatment with high dietary protein level showed the highest count for different zooplankton groups, especially for total Protozoa. Protozoa taxa showed a significant regression model (R²_adjusted= 0.814, P<0.001) relation with both TSS and nitrogen input. While, the total rotifers showed no correlation with any of the independent variables except for a polynomial relation with Alona  intermedia,(P= 0.01). The only cladoceran species recorded in the water samples was Alona  intermedia and it showed a significant regression model (R²_adjusted = 0.363, P<0.001) with Phosphorus input and alkalinity. Phosphorus input and alkalinity seemed to explain 56% of the copepods count (P=0.003). Ostracoda species showed a significant positive relationship with both energy input and Protozoa species of Centropyxis aculeate ( R²_adjusted =0.302 P= 0.003). It could be concluded that alkalinity, TSS, and mineral input are the major variables that affected the zooplankton community density, especially the large-sized groups.