Clams, Meretrix meretrix, were one of the favorite aquatic products in Taiwan and the world. It was reported that the water pollutants such as heavy metals and chemicals might accumulate in the clam body and shell through filter-feeding behavior. Thus, the bivalves could be used as bioindicators in the aquatic environment. The present study analyzed 20 trace elements, Mg, Sr, Li, Cd, Ba, Mn, Al, U, Ti, Pb, Nd, B, S, Zn, Fe, P, Na, K, Cu, and Ni, in the shells of the clams collected from the wild coastal area and cultured ponds to evaluate which elements have the potential to be biomarkers. The concentrations of 20 elements were detected by Solution-Based Inductively Coupled Plasma Mass Spectrometry (SB-ICPMS). Among them, Cd, Al, U, Ti, Nd, S, and K were below the detection limit. The remaining elements were analyzed for accumulation. The levels of Zn, Fe, and Ni possess high variation in an identical environment; so, a PCA was conducted without these three elements to reduce noise. The PCA result proved that the clam could absorb specific trace elements from the habitat. After a period of time, the contents of the absorption in the shells of the clams living in an identical environment became more similar. The analyzed element, Pb, was not found with a special difference in this study. The levels of Na, Sr, Mg, B, Mn, P, Ba, Li, and Cu reflected different sampling sites, which suggested that these elements in the species M. meretrix had the potential to be used as biomarkers for assessing heavy metal accumulation in the environment.