This study concerns using Multivariate statistical analysis to handle the large complex datasets in lakes and use water quality index factor to estimate the water quality in lakes. This study investigated the seasonal and spatial variations of water quality parameters in Burullus Lake in Egypt as a case study. Significant seasonal changes (p < 0.05) were observed in temperature, pH and phosphate (PO 4-P), whereas significant spatial differences (p < 0.05) were detected in pH, salinity, dissolved oxygen (DO), ammonium-nitrogen (NH 4-N), nitrite-nitrogen (NO 2-N), nitrate-nitrogen (NO 3-N), PO 4-P, silicate (SiO 4) and Chlorophyll-a (Chl-a). The water quality index (WQI) estimated using the inputs of: salinity, DO, NH 4-N, NO 3-N, PO 4-P, and Chl-a. The (WQI) of the lake was rated as "Bad" to "Very bad". Based on principal component analysis (PCA), the first principal component (PC1: 38.78%) represented high loadings on NH 4-N: 0.46, NO 3-N: 0.45, and PO 4-P: 0.45, indicating that the lake was mainly influenced by nutrients concentrations coming from agricultural lands. The results from cluster analysis and a dendrogram indicated that Burullus Lake was mainly influenced by spatial variations rather than seasonal changes.