The chlorophyll fluorescence imaging technique is a valuable tool for studying the impact of heavy metal stress in plants. The toxic effects of cadmium (50 mg/kg soil) and arsenic (5 mg/kg soil) on growth and the photosynthetic apparatus of two soybean cultivars (Glycine max (L.) Merr. cvs. Bólyi 44 and Cordoba) were assessed. After 10 days of growth in the contaminated soil, fresh and dry weights of shoots and maximum quantum yield of photosystem II (F v /F m ) for the three types of leaves (UL-unifoliate leaf, TL1-first fully expanded trifoliate leaf, TL2-newly expanding trifoliate leaf) were determined. No statistically significant change in the growth parameters was recorded. In the youngest leaves (TL2) of cultivar Bólyi 44, arsenic caused decrease in F v /F m by 8.6%. In the cultivar Cordoba we recorded the arsenic impact, conversely, having the highest inhibition rate of fluorescence in the oldest leaves (UL decrease of 5.62%). A similar difference in trend of changes in F v /F m as the impact of cadmium was also recorded. With the Bólyi 44 variety, the TL2 leaves showed most sensitive response (a decrease of 10.75%); while in the case of Cordoba variety TL2 leaves showed the highest tolerance (a decrease of 1.2%). The results suggest possible genotypic differences in defense strategy against cadmium and arsenic in the different types of leaves.