This study was carried out to investigate the seasonal variability and distribution of heavy metals “HMs” (Fe, Mn, Co, Cr, Cu, Ni, Pb, Zn and V) in the bottom sediments of Lake Qaroun, in Egypt. The samples were collected from 10 sites in summer and winter seasons in 2015. Total metals concentrations were measured using inductively coupled plasma spectrometer. Multivariate techniques were applied to analyse the distribution and potential source of heavy metals. The mean seasonal concentrations follow a descending order of Fe > Mn > V > Zn > Cr > Ni > Cu > Co > Pb. The mean concentrations of HMs in sediments during summer were higher than the concentrations during winter and above the average world shale values, except for Pb, suggesting potential adverse toxicity to aquatic organisms. All metals showed enrichment during summer and winter at sites S3 and S5 in the southeastern parts of the lake due to the heavy discharge of contaminants from El-Bats and El-Wadi drains. Principal component analysis results suggested two principal components controlling HMs variability in sediments, which accounted for 63.9% (factor 1: Co, Cr, Cu, Ni, Zn, Pb and V), 15.9% (factor 2: Mn and Fe) during summer, and 76.7% (factor 1: Fe, Co, Cr, Cu, Ni, Zn, Pb and V), 13.8% (factor 2: Mn) during winter of the total variance. Geo-accumulation index (Igeo) showed some pollution risk at the southeastern and southern parts (sites S3 and S5). Dilution during winter, concentration during summer, impact of non-point sources from different agricultural, industrial, municipal sewage and fish farms in the southern part of Lake Qaroun, adsorption and salt dissolution reactions and lithogenic sources are the main controlling factors for HMs in the study area. Monitoring of contaminant discharge at Lake Qaroun should be introduced for future remediation and management strategies.