Abstract Water system closure in recycled containerboard mills may have reached a technical limit due to the accumulation of organic and inorganic contaminants in the process water. The specific water chemistry characteristics of recycled containerboard mills with restricted water systems were analyzed and a computer model was developed to simulate calcium carbonate solubility in the presence of volatile fatty acids under relevant mill conditions. A strong linear correlation between VFAs and calcium ions was found. The calcium carbonate dissolution mechanism, solubility, and precipitation were investigated. The reaction of VFAs with calcium carbonate results in the formation of bicarbonate and carbonic acid. By binding hydrogen ions, the carbonate has a pH buffering effect. The carbonic acid dissociates into water and CO2. Gaseous CO2 escapes from the water and leads to decarbonization. This mechanism is responsible for the uncoupling of pH from the concentration of VFAs, as well as from the concentration of dissolved calcium ions. The resulting lack of carbonates prevents the precipitation of calcium carbonate. The introduction of CO2 contained in the biogas produced in anaerobic biological water treatment reverses the dissolution mechanism and causes the precipitation of calcium carbonate. Concentrating technologies such as membrane filtration and evaporation may therefore meet the specific requirements for complete water system closure in recycled containerboard mills better than current commonly used biological treatment.