Based on the method of combined determination and light scattering, we studied the effect of organic matter on the surface charge properties of soil colloidal particles and condensation process of colloidal particles in water bodies. The results showed that the addition of organic matter significantly changed the surface charge properties of soils, because of the total charge number increased about 6.8%, the specific surface area decreased about 12.3%, and organic matter addition decreased the surface charge density of the particles and the surface potential. Further theoretical calculations showed that the addition of organic substance reduced the electrostatic repulsion between colloidal particles, which made the net gravity increase and aggregation of soil colloids become easier. The aggregation characteristics of soli colloids in the water bodies were studied by the method of light scattering, the results showed that the critical coagulation concentration (CCC) was 91.6 mmol/L before removing organic matter, and it was 139.3 mmol/L after organic matter was removed, and the difference betweent these two values was significant. The critical surface potentials for colloidal particle dispersive or aggregate were both about -150.0 mV at the corresponding concentrations. And the above concentrations were the critical concentrations that net gravitational attraction appeared between particles. The effect of organic matter on the aggregation characteristics of colloidal particles in water bodies was mainly through changing surface properties and the corresponding interactions of particles.