The large-scale production and usage of zinc oxide nanoparticles (ZnO NPs) may lead to their post-release into the aquatic environment. In this study, the effect of hydrophobic/hydrophilic organic ligands on sorption and sedimentation of ZnO NPs has been systematically investigated. In addition, the coagulation efficiency of ZnO NPs, Zn2+, dissolved organic carbon (DOC), and UV254 with varying ferric chloride (FC) dosages in synthetic waters were also evaluated. The results showed that the higher concentration of organic ligands, i.e., humic acid (HA), salicylic acid (SA), and L-cysteine (L-cys) reduced the ζ-potential and hydrodynamic diameter (HDD) of particles, which enhanced the NPs stability. The adsorption of organic ligands onto ZnO NPs was fitted with the Langmuir model, with maximum adsorption capacities of 143, 40.47, and 66.05 mg/g for HA, SA and L-cys respectively. Removal of up to 95% of ZnO NPs and Zn2+ was achieved in studied waters at the effective coagulation zone (ECR), above which excess charge induced by coagulant restabilized the NPs in suspension. Moreover, the removal rate of DOC and UV254 were found to be higher in hydrophobic waters than hydrophilic waters. The width of ECR strongly depends on the characteristics of source water. The waters with hydrophobic ligand and higher UV254 values require more coagulant than hydrophilic waters to achieve the similar ZnO NPs and Zn2+ removal. The results of Fourier transform infrared (FT-IR) analysis of ZnO NPs composite contaminant flocs indicated that the combined effect of enmeshment and charge neutralization might be a possible removal mechanism. These findings may facilitate the prediction of fate, transport, and removal of ZnO NPs in the natural waters, and might contribute to risk assessment, as well as decision making about engineered nanoparticles (ENPs) in aquatic systems.