Distribution of 16 trace and minor chemical elements was examined ontogenetically with PIXE in the calcitic-prismatic margin of the shell of genetically close individuals of Crassostrea virginica (Gmelin) growing in three different marine habitats. Concentration of elements was also related to that in ostreid soft tissues and in suspended sedimentary particles in the ambient seawater. Distribution of the elements (Na, Mg, Al, Si, S, Cl, K, Ca, Ti, Mn, Fe, Ni, Cu, Zn, Br and Sr) was analyzed every 4 weeks (from May to November) with a non-destructive probe (PIXE) in newly deposited shell of the left valve, and in pigmented, non-pigmented and the right valve of 30 living C. virginica grown for 28 weeks in three dissimilar environments (10 oysters in each habitat): closed laboratory mariculture (HI), closed laboratory mariculture plus suspended sediment (HII) and natural flowing estuary (HIII). The same elements were analyzed weekly in suspended particles (on 0.4 μm Millipore filters) in the culture seawater in HI and HII and in ambient seawater in HIII; and at the end of the study in gills, adductor muscles, gonads and tissues of whole oysters. Elements in suspended sediment were concentrated primarily on the particles; not in the seawater filtrate. Barite crystals were present in some of the plankton samples. Growth rate was slowest in HI oysters, that of HII and HIII was similar and greater than that of HI. Seasonal trends in concentration of elements in valves in the different habitats varied. Ti remained relatively constant in HI valves during culture, but tended to decrease in HII, and increased in HIII. Other elements in HI tended to remain constant (Cu), or to increase (Fe); in HII some elements decreased conspicuously; in HIII some increases were prominent (Mg, Zn). A temporal change in level of many elements in shell paralleled that of the same element in suspended particles (Fe in HI, Mg, Cu, Zn in HIII); levels decreased in HII (Al, Ti, Fe). Parallelism of elemental concentration in shell and suspended particles was expressed as major peaks in both, mostly in HIII, the natural estuarine setting. For Ni, Cu, Zn and Br, especially in HII, peaks were out of phase. Comparison of concentration of elements in old (4th week of culture) and new (28th week) shell showed some trends among the three habitats; consistent association was evident in 10 elements in HIII. Maximal concentration of most elements occurred in the right valve. Pigmented shell contained slightly higher levels of most elements, but differences were only suggestive. After 28 weeks of culture, soft tissues contained several times the concentration of elements, and greater variability, than shell. Maximal concentration (biomagnification) of 13 elements took place in gills, gonads and adductor muscles, but not in whole oysters. There were clear differences in concentration of many of the elements among gills, gonads and adductor muscles in HI, HII and HIII, decreasing or increasing incrementally from HI to HII. Concentration of a few elements was associated in shell and tissues: in shell in HI, Fe, and in HIII, Zn increased during the 28 weeks and was also maximal in the three organs at the end of the study. All other elements (less Ca, Mn and Sr) were more concentrated in tissues than in shell, Zn, Cl and Br to a high degree. The relationship between biomagnification in different organs and the different microstructures of the shell is still unclear. The investigation focused on ecological aspects of biomineralization in living bivalves, an aspect little studied in the past. It was made possible by the use of the non-destructive PIXE probe and suggests a model from which to initiate further comparative studies.