River Atoyac is considered to be one of the most polluted rivers in Mexico due to the discharges of untreated or partially treated wastewater from industrial and municipal activities. In order to improve the river water quality, it is obligatory to identify the possible contaminant sources for upholding a well-balanced ecosystem. Henceforth, the present study incorporates the application of a continuous real-time monitoring system to identify the provenance of pollutants of the river mainly from anomaly events. Four monitoring stations were installed all along the River Atoyac in the State of Puebla, Central Mexico. The real-time monitoring systems have an ability to measure various water quality parameters for every 15 minutes such as Temperature (T), pH, Conductivity (EC), turbidity (TURB), Dissolved Oxygen (DO), Oxidation Reduction Potential (ORP) and Spectral Absorption Coefficient (SAC). In total, eight water samples of anomaly events (i.e.) 2 per monitoring station during rainy (August–September) and winter seasons (November–December), that were detected using the parameters previously mentioned were procured and also analyzed in the laboratory for evaluating almost 54 physicochemical, inorganic and organic characteristics. Statistical results of factorial analysis explained that 30% of the total variance corresponded to textile effluents, 23% related to discharges produced by automobile and petrochemical industries, and 18% of the total variance defined the agricultural activities. Additionally, indices like Overall Index Pollution, Heavy Metal Evaluation Index, Screening Quick Reference Table and Molecular ratios of hydrocarbons for PAH sources was also calculated to estimate the grade of pollution and associated ecotoxicological risks. The present study also enlightens the fact that the assessed results will definitely provide valuable information for the management of river water quality by developing stringent public policies by governmental agencies for the sustainable conservation of Atoyac River.