This study was carried out on Lake Qarun and 2 drains (El-Batts and El-Wadi) that discharging wastewater into it, at Fayoum Province, Egypt,  to assess the Water Quality Index (WQI) and miicrobial loadof their waters. This investigation was conducted during the period from autumn 2017 to summer 2018. The general annual averages of WQI values of Lake Water were poor for irrigation (69.61) and very poor for aquatic life (78.53). El-Batts and El-Wadi Drains were poor both for irrigation (55.45) and for aquatic life (54.45). Moreover, total viable bacteria count (TVBC) at 22°C ranged between 3 ×10³ CFU/ml and 450 × 10³ CFU/ml, and  the TVBC at 37°C varied from 0.4 ×10³ CFU/ml to  330 ×10³ CFU/ml .  Total coliform (TC) in the range of 0.3 ×10³ - 46 × 10³ MPN /100ml water , Fecal coliform (FC) in the range of 3×10²- 460× 10² MPN /100ml water . Fecal streptococci (FS) in the range of 3 × 10² - 1100 × 10² MPN/ 100ml water and the numbers of E.coli fluctuated between 0.1×10² and 60 × 10² CFU /100ml water. The obtained values of physical, chemical and microbial parameters of Lake and drains water were compared with the standard values set by FAO (1994)for irrigationand CCME (2007) for aquatic life. It was found that the values of tested parameters were higher than the recommended standards and this affects the biota in the studied area and  is expected to cause healthy problems.