In this research, the modified Canadian water quality index (MCWQI) was successfully applied with other common sediment indices for quality assessment of sediments from two Egyptian Mediterranean harbours: Port Said (PS), and Damietta Harbour (DH). The geochemical analysis demonstrated the dominance of the sandy-mud texture for PS sediments, while it was muddy for DH sites. Organic carbon, and total phosphorus in DH (0.46%; 1.08%) were slightly higher than in PS (0.32; 1.07%), while total carbonate was higher in PS (12.12%) compared to DH (10.63%). Eight heavy metals (HMs) showed a similar order of abundance with higher records in DH for HMs (except Pb). Ecotoxicologically, HMs levels were lower than the effects range low (ERL), suggesting no adverse effects; however, Ni and Cr might cause impacts up to 40 - 90% (> effects range median; ERM), particularly in DH. Environmental indices (e.g., MCWQI) revealed that sediments of DH were more contaminated than PS, with a marginal (∼ 59%) and a fair (∼ 70%) quality, respectively. Statistically, good correlations with a noticeable trend of loadings among studied parameters were recognized in PS, compared to DH. The study emphasized the vital roles of the topography, current movement, and levels of activities, that control the distribution of contaminants, pollution status and hence sediment quality.