El-Umum Drain has been identified as a significant pollution source, consistently discharging drainage water into the southeastern Mediterranean Sea at El-Mex Bay in Egypt. Hence, El-Mex Bay water and its drain were extensively studied. Nevertheless, the previous assessments did not consider the relative weights of the measured variables, which would overlook the seasonality and potential improvements of the water quality due to the enhancement of wastewater treatment techniques. In this study, a modified water quality index (WQI) and multivariate analysis were applied to accurately assess the water quality of El-Mex Bay and El-Umum Drain. Water quality parameters at nine stations were measured during 2020-2021. Most of the parameters showed significant spatial and temporal variations, indicating the influence of anthropogenic activities. The WQI values ranged from “poor" in El-Umum Drain to “medium" in El-Mex Bay open water.  The cluster analysis (CA) was employed to categorize the nine survey sites into three distinct groups. Specifically, the analysis revealed highly polluted stations at El-Umum Drain and moderately polluted stations in the El-Mex open water area. In addition, the CA classified the sampling months into two groups: highly polluted in March, May and August, and less polluted in January, indicating the variation of the volume of the discharged wastewater. Principal component analysis/factor analysis revealed that the parameters responsible for water quality variations were mainly associated with the inorganic dissolved nutrients, salinity and organic matter (anthropogenic).  The application of the modified Water Quality Index (WQI) enabled an accurate and scientifically rigorous evaluation, even when individual variables experienced deterioration or improvement. This approach addresses the limitations of previous evaluation methods that relied on single-factor assessments, providing a more comprehensive and nuanced understanding of water quality conditions.  For future water quality monitoring, it is recommended to apply the modified Water Quality Index (WQI) and include additional variables such as heavy metals and fecal bacteria. This approach would result in more comprehensive and scientifically sound evaluations.