A monitoring program enabled the evaluation of water quality and the simulation of the pollution dynamics of the rivers in the Joya de los Sachas and Francisco de Orellana cantons in Ecuador. For this assessment one used the WQI (water quality index) and the pollution indices ICOMO (organics contamination), ICOSUS (suspended solids), ICOMI (mineralization), ICOTRO (trophy system), and ICOpH (pH Index). The mathematical model operates with several input parameters, including dissolved oxygen, fecal coliforms, the biochemical oxygen demand (BOD5), turbidity, total solids, total phosphorus, pH, total nitrogen, suspended solids, alkalinity, conductivity, temperature, and the concentrations of nitrates, nitrites, and phosphates. WQI values were obtained from ICO pollution indices. The pollution of the Sacha area is significant, WQI = 0.292, which represents an advanced degree of pollution, since increased BOD values correspond to a high load of organic pollutants. They can originate from household, agricultural, industrial, and soil erosion waste. Likewise, the Sacha River has an ICOSUS = 0.16, which renders water treatment difficult, without impacting human health. Calculated WQI values reveal that the water quality of the Sacha, Basura and Coca rivers is low, being highly contaminated. In contrast, the Huamayacu, Jivino Rojo, Jivino Negro, and Jivino Blanco rivers are commonly polluted.