Soil sodicity is widespread in the cracking clays used for irrigated cotton (Gossypium hirsutum L.) production in Australia and worldwide and sometimes produces nutrient imbalances and poor plant growth. It is not known whether these problems are due primarily to soil physical or to soil chemical constraints. We investigated this question by growing cotton to maturity in a glasshouse in large samples of a Grey Vertosol in which the exchangeable sodium percentage (ESP) was adjusted to 2, 13, 19, or 24. A soil-stabilising agent, anionic polyacrylamide (PAM), was added to half the pots and stabilised soil aggregation at all ESPs. Comparison of the effect of ESP on cotton in the pots with and without PAM showed that, up to ESP of 19, the soil physical effects of sodicity were mainly responsible for poor cotton performance and its ability to accumulate potassium. At ESP >19, PAM amendment did not significantly improve lint yield, indicating that soil chemical constraints, high plant sodium concentrations (>0.2%), and marginal plant manganese concentrations limited plant performance. Further research into commercial methods of amelioration of poor physical condition is warranted rather than application of more fertiliser.