A large number of white hard clam farms are in the estuary shoreline of Saigon-Dongnai Rivers, which flow through Ho Chi Minh City, a megacity, and numerous industrial zones in the basin catchment area. In this study, eleven trace elements (Mn, Fe, Co, Ni, Cu, Zn, As, Se, Cd, Hg, and Pb) in the hard clam Meretrix lyrata and its habitats including surface water, suspended particulate matter, and sediment were evaluated to understand the bioaccumulation of trace metals from the environment into the whole tissues of the hard clam as well as its different organs. The samples were collected monthly in dry, transition, and wet seasons of the southern part of Vietnam from March to September 2016. The results showed that seasonal and spatial variations of the studied metal concentrations in the hard clam M. lyrata might be influenced by the sea current as well as the surface runoff in the rainy season. The relationship between condition index and the element concentrations in M. lyrata might be affected by the living environment conditions and farming methods. In addition, the hazard index values of all trace elements in the hard clam M. lyrata harvested in the sampling time show that the hard clams farmed in the study area were safe for local consumers.