Background and aims Plant species composition in wetlands and on lakeshores often shows dramatic zonation which is frequently ascribed to differences in flooding tolerance. This study compared the growth responses to water depth of three species (Phormium tenax, Carex secta, Typha orientalis) differing in depth preferences in wetlands, using non-linear and quantile regression analyses to establish how flooding tolerance can explain field zonation. Methodology Plants were established for 8 months in outdoor cultures in waterlogged soil without standing water, and then randomly allocated to water depths from 0 – 0.5 m. Morphological and growth responses to depth were followed for 54 days before harvest, and then analysed by repeated measures analysis of covariance, and non-linear and quantile regression analysis (QRA), to compare flooding tolerances. Principal results Growth responses to depth differed between the three species, and were non-linear. P. tenax growth rapidly decreased in standing water > 0.25 m depth, C. secta growth increased initially with depth but then decreased at depths > 0.30 m, accompanied by increased shoot height and decreased shoot density, and T. orientalis was unaffected by the 0 – 0.50 m depth range. In P. tenax the decrease in growth was associated with a decrease in the number of leaves produced per ramet and in C. secta the effect of water depth was greatest for the tallest shoots. Allocation patterns were unaffected by depth. Conclusions The responses are consistent with the principle that zonation in the field is primarily structured by competition in shallow water and by physiological flooding tolerance in deep water. Regression analyses, especially QRA, proved to be powerful tools in distinguishing genuine phenotypic responses to water depth from non-phenotypic variation due to size and developmental differences.