During commissioning and process stabilization of a NDBEPR plant at Bendigo intracellular distribution and movement of phosphorus, K+, Mg2+ and Ca2+ was followed to establish the nature of biomass development. The system was also monitored at the end of a period of breakdown of the BEPR process and during its return to phosphorus removal. Phosphorus (P) and Mg2+ distribution in the biomass were closely related during all phases of plant operation, and laboratory trials indicated that the poor performance of the full-scale plant was associated with seasonal reduction in influent Mg2+. Laboratory scale trials produced a similar effect when the influent Mg2+ was limited to concentrations much lower than those experienced in the full scale plant, but only after the Mg2+ and P reserves in the biomass were depleted. The distribution of P, K+, Mg2+ and Ca2+ in the biomass from the full scale plant was similar to that seen in the laboratory trials when cations in the feed were severely limited and recovery of the full scale plant also closely matched that of the laboratory scale system.