Modern municipal wastewater treatment often includes an anaerobic digestion step with a hydraulic retention time of ~1.5 days before the main anaerobic digestors. This step, often termed the organic acid digester or “acid digester” for short, produces a sludge characterized by lower pH, higher volatile fatty acid (VFA) concentrations, and high soluble phosphorus (P) concentrations, particularly if fed sludge from an enhanced biological phosphorus removal process. Here, the analysis of major ions, organic and inorganic, in the organic acid digest from a wastewater treatment plant (WWTP), Nine Springs, Madison, Wisconsin (USA), is reported for a period of 13 weeks. The bioengineered origin of this organic acid digest makes its composition unlike natural waters of any kind. From the chemical composition, the course of subsequent processes can be predicted by chemical modelling. Methanogenesis using VFAs as substrates is predicted to raise digest pH to the point where struvite is expected to form, and nuisance struvite is routinely observed at Nine Springs. Addition of calcium hydroxide to organic acid digest is expected to precipitate ~90% of soluble P from solution as the calcium phosphate mineral brushite at near neutral pH, confirmed by a pilot plant at Nine Springs. This study demonstrates the possible application of chemical analysis and chemical modelling in wastewater systems to predict and possibly adaptively manage waste streams to curb nuisance struvite formation and predict P recovery, and could be refined through broader testing and application at other wastewater treatment facilities.