The aim is to examine the nutrient ion dynamics in a Vertisol soil undergoing waterlogging to ascertain whether soil solution concentration and/or nutrient uptake dynamics are the cause of boll shedding in cotton. Cotton was grown in pots, and the soil waterlogged after 76 days at which time injections of 33P and 86Rb were made to trace phosphorus (P) and potassium (K) dynamics. After seven days, waterlogging in the pots were drained and an injection of 32p was made to trace P dynamics during the recovery period. Redox fell rapidly during waterlogging, and soil solution concentrations of P, K, sodium (Na), and manganese (Mn) increased. Biomass accumulation was less in the waterlogged treatment than in the non-waterlogged control. In the 7-day recovery period, shoot biomass increased in the waterlogged treatment and root biomass weight continued to decline. Recovery of 33P was 10 times higher in the control than in the waterlogged treatment during the 7-day waterlogging period treatment. Uptake of 86Rb in the control treatment was more than twice that of the waterlogged treatment during this period. Uptake of both33P and 86Rb increased during recovery but remained higher in the control treatment. Uptake of 32p occurred during post-waterlogging but remained higher in the control treatment. Reduced uptake of P and K during waterlogging is most likely due to damage to the uptake mechanisms of the roots rather than a reduction in the concentration of nutrients in the soil solution under waterlogged conditions.