In an effort to minimize the impact on the environment or improve the properties of choice, most engineered nanoparticles used for commercial applications are surface functionalized. The release of these functionalized engineered nanoparticles (FENPs) into the environment can be either deliberate or accidental. Scientific research to date has tended to focus on evaluating the toxicity of FENPs, with less attention being given to exposure assessments or to the study of their general behavior in natural environments. We have therefore investigated the effects of environmental parameters such as pH, NaCl concentration, and natural organic matter concentration on the aggregation kinetics of FENPs with time resolved dynamic light scattering, using functionalized gold nanoparticles (FAuNPs) as a representative of these particles. We also investigated the effects of average particle size, the type of surface capping agent, and particle concentration on FAuNP aggregation kinetics. Our results show that the physico-chemical properties of the capping agent have a greater influence on the aggregation behavior of FAuNPs than either their core composition or their particle size.