* Incomplete denitrification is often observed in the B-stage if the influent C/N ratio is low. Direct by-pass of a part of A-stage influent with high organic matter content to the B-stage is used to increase the C/N ratio.
* High sludge production in the A-stage is a drawback for WWTPs that are not equipped with anaerobic digestion of sludge because it increases sludge treatment costs.
* Sludge from A-stage has poor settling properties.
* High retention times cause an increased need for additional reactors to maintain throughput increasing equipment costs