Biotests conducted with plants are presently used to estimate metal bioavailability in contaminated soils. But when plants are grown in soils, especially the plants with fine roots, root collection is easily biased and tedious. Indeed, at harvest, small amounts of soil can adhere to roots, resulting in overestimation of root metal content, and the finest roots are often discarded from the analysis because of their difficult and almost impossible recovery. This report presents a novel method for assessing the bioavailability of heavy metals in soils using microalgae. Two species of green unicellular microalgae were isolated from two highly contaminated soils and identified by phylogenetic and molecular evolutionary analyses as Chlorella sp. RBM and Chlorella sp. RHM. These two cultures were used to determine the metal uptake from metal-contaminated soils of South Australia as a novel, cost-effective, simple and rapid method for assessing the bioavailability of heavy metals in soils. The suggested method is an attempt to achieve a realistic estimate of bioavailability which overcomes the inherent drawback of root metal contamination in the bioavailability indices so far reported.