Six wheat varieties with different tolerance to waterlogging were studied in acidic soil (pH 4.5), neutral soil, and potting mix (pH 6.7-7.8) under controlled conditions. Waterlogging for 49 d reduced shoot dry weight by 48% to 85% compared with drained treatments. The ranking of varieties for waterlogging changed under different soils, and this change explains why waterlogging tolerance of these varieties may vary in different environments. In waterlogged acidic soil, shoot concentrations of aluminum (Al), manganese (Mn), and iron (Fe) increased by two- to 10-fold, and in some varieties they were above critical concentrations compared with plants in drained soil. These elements decreased or remained the same in shoots of plants grown in waterlogged neutral soil. Marginal nitrogen (N) deficiency was induced in most varieties in all soil types. The results support the importance of screening in soils from the target environment for accurate germplasm characterization for waterlogging tolerance.