A method and knowledge-based system for generating a holistic health index for diagnosis and decision support in operational management of biological treatment of waste water with a microbial population; measured parameters of an operating biological treatment employing a microbial population are compared with benchmark values in a data base to generate a comparison value and a holistic health index of the operating microbial population is generated from the comparison values which provide an evaluation of the operational management of the biological treatment. Based on such evaluation the operating parameters of the treatment may be adjusted to maintain the treatment at an optimum level.
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