High-molecular-weight anionic polyacrylamide was used to analyze the effect of kaolin on the structure of particle aggregates formed in freshwater and seawater. Batch flocculation experiments were performed to determine the size of the flocculated aggregates over time by using focused beam reflectance measurements. Sedimentation tests were performed to analyze the settling rate of the solid–liquid interface and the turbidity of the supernatant. Subsequently, a model that relates the hindered settling rate to the aggregate size was used to determine the mass fractal dimension (𝐷𝑓). Flocculation kinetics revealed that greater amounts of kaolin generated larger aggregates because of its lamellar morphology. The maximum size was between 10 and 20 s of flocculation under all conditions. However, the presence of kaolin reduced the settling rate. The fractal dimension decreased with the increase in the kaolin content, resulting in the formation of irregular and porous aggregates. By contrast, factors such as the flocculation time, water quality, and quartz size had limited influences on the fractal dimension. Seawater produced a clearer supernatant because of its higher ionic strength and precoagulation of particles. Notably, the harmful effect of clays in seawater was reduced.