Plant nutrient acquisition is dramatically reduced in sensitive species when in waterlogged soil. Upon waterlogging, root growth can be immediately arrested whereas shoots can continue to grow. The resulting increased shoot:root ratio causes an imbalance between shoot nutrient demands and supply by roots. Nutrient ion uptake be roots is also greatly reduced on a per root weight basis (Elzenga and van Veen 2010; Colmer and Greenway, 2011), primarily as a result of reduced O₂ availability inhibiting respiration. Ion uptake by roots consumes energy. The plasma membrane proton pump (H⁺-ATPase) requires ATP and the proton motive force generated is used to drive symporter-mediated ion uptake. Indeed, all anions (e.g. NO₃^-) enter root cells via H⁺-anion symporters. Furthermore, the H⁺-ATPase maintains the negative membrane potential, essential to creating electrochemical gradients allowing channel-mediated uptake of cations (e.g. K⁺ uptake). Absence of O₂ inhibited respiration and lowered H⁺-ATPase pumping, causing a substantial membrane depolarization, making such cation uptake via channels thermodynamically impossible (Pang and Shabala 2010). Not only is K⁺ uptake significantly reduced, but roots can also loose substantial amounts of K⁺ through depolarization-activated channels. It is not surprising, therefore, that waterlogged plants often exhibit acute K⁺ deficiency. The organic acids present in waterlogged soils, from anaerobic microbial metabolism, can also lead to membrane depolarisation of root cells and reduced ion uptake.

The diminished capacity for ion transport, together with initial ‘dilution’ of shoot nutrient concentrations by continued shoot growth relative to roots, explains a range of nutrient deficiencies observed in leaves of intolerant plants under waterlogged conditions. Waterlogging tolerant species with adequate O₂ supply to roots via large volumes of aerenchyma, can sustain root respiration and therefore plasmamembrane H⁺-ATPase functioning for nutrient uptake, as well as having adequate O₂ and energy for deeper root penetration. Efficient internal aeration of roots, together with a barrier to ROL in basal zones, also enables an aerobic rhizosphere at the root tips and regions of dense laterals, altering the rhizosphere (e.g. diminished soil toxins), presumably also with benefits for nutrient uptake by the roots.