Potential use of hydroxyapatite nanoparticles (HANPs) [Ca10(PO4)6(OH)2] as slow P-release fertilizer (SRF) has recently attracted wider attention. However, commercially available HANP (with Ca/P ratio = 1.667) is the least soluble calcium phosphate and thus limits its full potential as an SRF in agronomic applications. In this research, we sought to enhance the dissolution rate of HANPs by enriching hydrogen phosphate (HPO42−) species in the phosphate (PO43−) structural sites. Seven different types of pure crystalline HANPs were synthesized at a range of Ca/P ratio from 1.46 (at pH 6.0) to 2.10 (at pH 12.0). Complementary results from FTIR and solid-state 31P MAS NMR spectroscopies showed that HPO42− species is most abundant in HANPs crystallized at pH 6.0 and gradually depleted at higher pH products. The rate of depletion of HPO42− species is proportional to the increase in carbonate incorporation into the HANP lattice, which preferentially forms B-type carbonated HANPs. The enhanced dissolution rate of HANPs due to hydrogen phosphate incorporation was tested using a flow-through macro-dialysis system that limits the partial transition of HANPs to other solid phases, which otherwise interfere with dissolution. The results show that the dissolution rate of HANPs increased with decreasing pH of synthesis and was highest in HANPs at pH 6.0. The dissolution rate differed by ten times between HANPs synthesized at pH 7.0 and 10.0. Overall, the atom-efficient synthetic route developed and the ability to tune the dissolution rate of HANPs are significant steps forward in improving the P-release efficiency of a potent SRF and is expected to contribute to efforts toward enhancing agricultural sustainability.