Root elongation method may be implemented using two internationally accepted protocols: exposing plants to either soil-water extract or whole soil. But which of the two protocols is more suitable for root elongation analysis undertaken for the quality assessment of metal-polluted soils? Soils were sampled at various distances from the site of the Middle Urals Copper Smelter located in Russia. White mustard was used as a bioindicator. We observed considerable differences in root elongation under the two protocols. In plants grown in whole soil, root length inversely correlated with pollution index, but in soil-water extract, metal concentrations had no effect on root length. Nutrient and metal concentrations in the soil-water extract were not buffered, due to the absence of the solid soil phase. It is for this reason that in highly polluted soils, root growth was greater in soil-water extracts rather than in whole soils, whereas in background soils (in the absence of toxicity), root growth was greater in whole soils compared with soil-water extracts. The quantity, intensity, and capacity factors are a plausible explanation for the differences in root length between the two protocols. The soil-water extract does not represent actual soil with respect to the desorption-dissolution reactions that take place between the soil solid phase and the soil solution. For this reason, whole soil protocol should be used for measuring root elongation given that only under this protocol, direct contact between metal-polluted soil and test organisms correctly replicates the risks inherent in the actual soil habitat. © 2020, Sociedad Chilena de la Ciencia del Suelo.