Many years ago the US EPA ...

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Many years ago the US EPA developed a protocol to answer your question for any given facility which involves conducting a Comprehensive Performance Evaluation (CPE) of the facility.   Their protocol with it's "scoring" of points is a bit simplistic but the overall method of assessing performance limitations across the Design, Management, Operations, and Maintenance dimensions of a target facility under consideration will identify performance limitations and provide directions on which to base effective troubleshooting and optimization efforts going forward.  I believe you can still get copies of the CPE approach from the EPA and I'd recommend it to anyone doing troubleshooting or hoping to optimize performance of water and wastewater treatment facilities.