Abstract Microorganisms, organic matter, heavy metals are the main pollutants in sewage water. The increasing water demand pressurized people to use the sewage water. Different systems, chemicals and physical treatments were used in sewage water treatment. The aim of this work is to study the effect and correlations of primary (Ca(OH)2 filtration and H2O2) and secondary (dissolved oxygen, organic matter, conductivity, pH and OD) factors on fungi present in sewage water in addition to proving the sequence of the system used in the current study. After treatment, fungi were examined, identified on Czapek agar and analyzed using multivariate tools (CANOCO: DCA and CCA) and R software. The treatment includes two main steps: liming filtration and oxidation, respectively. All parameters were negatively or positively correlated (organic matter, pH, conductivity %, optical density, fungal CFU ml-1, dissolved oxygen). Heavy metals were decreased due to the application of Ca(OH)2 and H2O2, respectively. There were two main groups of fungi. The larger was correlated with the organic matter, whereas the second was tolerating calcium hydroxide concentrations. Aspergillus sydowii tolerated hydrogen peroxide (0.2 mll-1(33%); Ca(OH)2, 0.25 gl-1). Sequential steps treatment was healthy and economically efficient. The proposed system improved water characteristics. The recommended amount of Ca(OH)2 and H2O2 was 0.25 gl-1 and 0.2 mll-1(33%), respectively, and can remove more than 99.9% of fungal CFUs. The current study minimized the optimum dose of hydrogen peroxide used in the disinfection of sewage water from 1.5 (Mohamed in Chem Eng J 119:161–165, 2006) to 0.2 mll-1 of H2O2 (the current study).