Improving the colloidal stability of magnetite nanoparticles (MNPs) is essential for their successful applications. In this study, the surface zeta potential and particle size evolutions of citric acid coated magnetite nanoparticles (CA-MNPs) were measured under varied aqueous conditions using dynamic light scattering (DLS). The effects of pH (5.0–9.0), ionic strength (IS), cations (Na+ and Ca2+), anions (phosphate, sulfate, and chloride) and humic acid on the aggregation behaviors of CA-MNPs were explored. Compared with bare MNPs, the stability of CA-MNPs were greatly improved over the typical pH range of natural aquatic environments (pH = 5.0–9.0), as the coated CA-MNPs were highly negatively charged over the pH range due to the low pKa1 value (3.13) of citrate acid. CA-MNPs were more stable in the presence of monovalent cation (Na+) compared with divalent cation (Ca2+), as Ca2+ could neutralize the surface charge of MNPs more significantly than Na+. In the presence of anions, the surface charges of CA-MNPs became more negative, and the stability of CA-MNPs followed the order: in phosphate > sulfate > chloride. The observed aggregation trend could be explained by the differences in the valences of the anions and their adsorption behaviors onto CA-MNPs, which altered the surface charges of CA-MNPs. The measured critical coagulation concentrations (CCC) values of CA-MNPs in these electrolyte solutions agreed well with Derjaguin–Landau–Verwey–Overbeek (DLVO) calculations. With the addition of Humic acid (HA), the aggregation of CA-MNPs was inhibited in all electrolyte solutions even with the critical coagulation concentrations. This is due to the adsorption of HA onto CA-MNPs, which enhanced the electrostatic and steric repulsive forces between CA-MNPs. Considering the good stability of CA-MNPs in solutions with varied pH and electrolyte compositions, as well as with the easy synthesis of CA-MNPs and their non-toxicity, this study suggested CA coating as a good strategy to increase the stability of MNPs.