Background A lab-scale anaerobic-anoxic/nitrification (A2N) two-sludge sequencing batch reactor (SBR) system was operated to assess the relationship among intracellular polymer conversions, bacterial population dynamics and nutrient removal performance in response to the varying influent COD/N/P. Results Complete nutrient removal was achieved in the A2N-SBR in Run 3 where the COD/P and COD/N were 20.6 and 6.9, respectively. This coincides well with the highest P release/HAc uptake ratio occurring in Run 3, confirming high abundance of denitrifying phosphorus accumulating organisms (DPAOs) in the biomass. Under the stress of N or P limitation, more poly--hydroxyalkanoates (PHA) was synthesized, with the increasing proportion of poly-hydroxyvalerate (PHV) in PHA. The population biodiversity decreased with increasing carbon loading when P loads were maintained at constant levels, and recovered to the initial level after P loading decreased. Conclusions Increasing COD/P promoted anaerobically synthesized PHA amount and favored P removal. Also, PHB seems to be the crucial internal carbon source relating to P release and uptake, whereas high nitrogen and P removal efficiencies always relate to a high proportion of PHV in PHA. Increasing carbon loading led to a decreased biodiversity of the community structure but favored higher PAO enrichments, if only P loading is not limited.(c) 2012 Society of Chemical Industry