In water-scarce areas, the reclamation of wastewater through advanced water treatment and subsequent reinjection into depleted aquifers is an increasingly attractive water management option. However, such injection can trigger a range of water-sediment interactions which need to be well understood and quantified to ensure sustainable operations. In this study, reactive transport modeling was used to analyze and quantify the interacting hydrogeochemical processes controlling the mobilization of fluoride and phosphate during injection of highly treated recycled water into a siliciclastic aquifer. The reactive transport model explained the field-observed fluoride and phosphate transport behavior as a result of the incongruent dissolution of carbonate-rich fluorapatite where (i) a rapid proton exchange reaction primarily released fluoride and calcium, and (ii) equilibrium with a mineral-water interface layer of hydrated dibasic calcium phosphate released phosphate. The modeling results illustrated that net exchange of calcium on cation exchange sites in the sediments postbreakthrough of the injectant was responsible for incongruent mineral dissolution and the associated fluoride and phosphate release. Accordingly, amending calcium chloride into the injectant could potentially reduce fluoride and phosphate mobilization at the study site. Insights from this study are broadly applicable to understanding and preventing geogenic fluoride mobilization from fluoride-bearing apatite minerals in many other aquifers worldwide.