The formation of flocs is crucial in the coagulation process of water treatment. However, the nature of ligand exchange on the surface of primary nanoparticles (PNPs) during floc formation requires further investigation to enhance our understanding of the coagulation mechanism. Phosphate (P) is a ubiquitous nutrient ion in aquatic surface water, in this study, the impact of P on floc growth under different pH conditions were investigated. The results revealed that floc growth patterns depended on both P dosage and pH. The mode of ligand exchange between P and in-situ formed ferric hydroxide within a pH range of 5 to 10 was further explored, and remarkable disparities in pH changes induced by P addition were observed. At lower pH levels, OH− release occurred relatively slowly, stabilizing with continued P addition. At neutral pH, OH− release was comparatively higher with P addition, while under alkaline conditions, both the quantity of OH− and its release rate decreased. It was deduced that triple bondFe–OH21/2+ sites function as "active sites," while triple bondFe–OH1/2− sites act as "inert sites" on the surface of PNPs formed during flocculation. These sites are crucial in the interconnections between flocs formed during coagulation and in floc growth. Analyses of Fe PNPs by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM), with and without P addition, revealed that the introduction of P inhibits or interferes with the self-crystallization of Fe PNPs through chemical coordination reactions. The results offer deeper insights into the coagulation mechanism and the transformation of Fe flocs in raw waters containing P during water treatment practices.