The stability and mobility of engineered nanoparticles in the natural water environment are influenced by various environmental factors, such as electrolyte conditions and the presence of natural organic matters. Cyanobacterial and microalgal extracellular polymeric substances (EPSs) are complex organic mixtures ubiquitous in eutrophic waters. In this study, bound EPSs (B-EPSs) and dissolved EPSs (D-EPSs) of Microcystis sp. and Chlorella vulgaris were extracted as the representative natural organic matters in the aquatic environment. Time-resolved dynamic light scattering and quartz crystal microbalance with dissipation monitoring were applied to investigate the influence of the extracted EPSs on zinc oxide nanoparticle (ZnO NP) aggregation and deposition behaviors. Data showed that EPSs with higher protein fractions were more efficient in hindering the aggregation of ZnO NPs in NaCl solutions and low CaCl2 concentration solutions. In higher CaCl2 concentration solutions (>50 mM), the presence of D-EPSs promoted aggregation by forming intermolecular bridging. By accelerating the Brownian movement of NPs and providing electrostatic and hydrophilic attraction between NPs and silica surfaces, B-EPSs facilitated ZnO NP deposition. On the contrary, D-EPSs hindered the deposition through steric repulsion. Moreover, B-EPS-coated ZnO NPs formed a more rigid layer, while the D-EPS-coated ZnO NPs formed a softer layer.