To better understand the fate and transport of ferrihydrite nanoparticles (FNPs), which carry many contaminants in natural and engineered aquatic environments, the aggregation of FNPs was systematically investigated in this study. The pH isoelectric point (pHIEP), surface zeta potential, and particle size evolutions of FNPs were measured under varied aqueous conditions using dynamic light scattering (DLS). The influence of pH (5.0 ± 0.1 and 7.0 ± 0.1), ionic strength (IS), electrolytes (NaCl, CaCl2 and Na2SO4), and organics (humic acid, fulvic acid and CH3COONa) on the aggregation behaviors of FNPs were explored. Meanwhile, Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was employed to better understand the controlling mechanisms of FNP aggregation. In the presence of sulfate, the surface charge of FNPs was neutralized under varied pH and ionic strength due to ion adsorption and FNPs phase transformation to schwertmannite based on FT-IR results. This phase transformation resulted in rapid aggregation in all water chemistries tested, whereas other salt species affected the aggregation primarily by ion adsorption and charge screening. Presence of increasing concentrations of the organic acids significantly shifted the pHIEP of FNPs (7.0 ± 0.2) to lower pH (< 4.0) due to adsorption of organics on FNPs surfaces making them negatively charged. The adsorption of HA/FA inhibited FNP aggregation significantly while CH3COONa did not, due to different effects on steric and/or electrosteric interactions among FNPs by organics with varied pKa values and molecular weights. After accounting for the important effects of pH, electrolytes, and organics in modifying FNPs' surface charge, DLVO calculations agreed well with measured critical coagulation concentrations (CCC) values of FNPs at both pH 5.0 ± 0.1 and 7.0 ± 0.1 in the presence of NaCl. This study will hence be useful to better predict and control the fate and transport of FNPs in the presence of electrolytes and organics with different molecular weights, as well as the fate of the associated contaminants in natural and engineered systems.