This study aims to assess the chemical and ecological quality of the marine ecosystem in Algerian central coastal zone (Bay of Algiers (AB) and Bou-Ismail Bay (BIB)) by examining several quality indicators of the marine ecosystem: water, sediment, and biota. Except for stations near the mouths of wadis and industrial and urban discharges released without prior treatment, the study of the physicochemical water quality in the different sampling stations revealed a more or less normal variation in temperature and salinity. According to nutrient salt analysis, all studied stations (in AB and BIB) have high nitrogen levels, such as ammonium and nitrate. However, low levels of phosphate were detected, indicating that this element is scarce in the Algerian coastal marine waters. Three trace metals were also analyzed in the sediments of both bays. Pb ranged from 21.15 to 52.69 μg g–1 dry weight (dw), Zn from 19.32 to 175.1 μg g–1 dw and Cd between 0.87 and 2.031 μg g–1 dw. Contamination factors ranged from 0.62 to 1.55 for Pb, 0.2 to 1.85 for Zn and 1.74 to 4.04 for Cd. Analysis of these three metals in sediment samples reveals their presence at most stations studied. The contamination index calculation shows a moderate anthropogenic intake that requires continuous monitoring to protect the study area’s ecosystem. Crucially, the analysis of fish products revealed a lack of chemical risk concerning trace metals, known for their detrimental health effects. However, this conclusion does not dismiss the potential for subtle contamination, warranting persistent environmental surveillance. Consequently, sustained efforts in environmental monitoring are imperative to ensure the preservation of the marine ecosystem amidst escalating anthropogenic pressures.