This present study seeks to investigate the impact of environmental variables on the mycotoxigenic fungi distribution in different stages of water treatment from Ede-Erinle and Opa water work systems. The sampling stations were grouped into raw, treated and distributed stations for each of the waterworks system and samples were collected on bi-monthly basis for one annual cycle, spanning through the rainy and dry seasons. A total number of 30 fungal species which belonged to 7 classes were isolated from both Ede and Opa water works systems during the study. This included 23 species from Ede water works and 14 fungal species from Opa water works system. Ascomycetes contributed 41.6% out of total fungal classes identified from Ede waterworks system followed by zygomycetes (33.3%), Deuteromycete (12.5%) while Penicillium and Mucor contributed 20.83% out fungal genera identified and aspergillus (16.67%). Zygomycetes accounted for 30.77% out of total fungal classes isolated from Opa waterworks system followed by ascomycetes (23.05%), Eusacomycetes and Dothideomycetes contributed 15.38% while Apsergillus, auerobasidium, rhizopus and cladosporium had the highest percentage contribution of 15.38% among the fungal genera identified. There was strong correlation between total Heterotrophic fungal distribution and water temperature and pH in water samples from Ede-Erinle waterworks systems that influenced the growth of mycotoxicin fungal while the nutrient parameters such as nitrate and phosphate influenced the abundance of fungi in water samples from Opa waterworks systems. In Ede-Erinle and Opa waterworks systems, the highest mean values for water temperature and phosphate were observed from distribution water while the mean concentration of pH and total heterotrophic fungal counts were higher in raw water samples. However, nitrate was higher in the treated water sample during the study. The presences of mycotoxigenic fungal such as Aspergillus sp, Mucor sp, Cladosporium sp., Penicillium sp., and Trichoderma sp from the treated and distribution water from Ede and Opa water work system after the water has undergo treatment process could pose serious health risks to consumers because they can cause aspergillosis, mucormycosis and penicilliosis infections respectively in human.