The aim of this study was to determine the levels of essential trace elements copper, zinc, manganese, and nickel in two size groups of mussels, Mytilus galloprovincialis, sampled from three sites along the Algerian coast with different levels of pollution. The results of this work are very interesting for determining the effect of mussel size on the variation of contaminant levels in environmental monitoring studies. Thirty individuals from 2 size groups, less than 4-cm and more than 4-cm shell length, were collected over 4 seasons at each site studied. The samples were dissected, and copper, zinc, manganese, and nickel were measured in the whole soft tissues by inductively coupled plasma mass spectrometry (ICP-MS). The maximum concentrations of copper, zinc, manganese, and nickel expressed in mg/kg dry weight at the three sites were 54.01, 146.25, 20.69, and 8.85, respectively. A clear distribution pattern of the studied elements was observed in the two size classes. In fact, significantly higher concentrations (P < 0.05) were found in individuals with a shell length of less than 4 cm. Significantly, higher concentrations (P < 0.05) were found in individuals with a shell length of less than 4 cm due to their high filtration and low excretion activities compared to long individuals. In addition, metal pollution index (MPI) values were higher in small bivalve individuals. The trace element contents found in the mussel samples of the present study showed large spatial and temporal variations among the different sites studied, highlighting the typical exposure of marine sites to different marine pollutants. Notably, elevated concentrations of copper were observed in the port of Zemmouri, likely due to port activities. Conversely, the highest levels of manganese and nickel were recorded at Boudouaou El Bahri, potentially attributable to the use of fertilisers by agricultural activities. Some shellfish samples had exceeded the permissible concentration levels of copper and manganese, thereby posing a danger to bivalve consumers.