The particulate matter composition in the Upper Cauca River section was studied, considering the importance of this river for the water supply of Cali, Colombia, and the implications that the turbidity of this water source has had for the city's water treatment. Additionally, the upstream Palo River was investigated, as this river is a major contributor to the Cauca River. River water samples were taken in both rivers in the period 2012–2014 during dry and rainy seasons. The origin of the particulate matter was studied through measurements of turbidity, total suspended solids (TSS), volatile suspended solids, particle size distribution, Fe3+, PO43−, NO3-N, chlorophyll-a, chemical oxygen demand, and true color. Turbidity and TSS values, measured during this survey, were highly variable, ranging from 25 to 465 NTU and 10 to 490 mg/L in the Cauca River, and from 30 to 840 NTU and 15 to 710 mg/L in the Palo River, respectively. High scattering was obtained in TSS and turbidity relationships in both rivers, potentially due to the different sources contributing to both parameters. It was concluded that the concentration of particulate matter depended merely on precipitation events in the Cauca and Palo River basins, leading to soil erosion due to extensive and intensive agricultural practices. In addition, the South Canal was identified as one of the main contributors to organic particulate matter.