A system is needed to predict the behavior, fate, and occurrence of environmental pollutants for effective environmental monitoring. Available monitoring data and computational modeling were used to develop a one-box multimedia model based on the mass balance of the emitted chemicals. Eight physiochemical phenomena in the atmosphere, soil, water, and sediment were considered in this model. This study was carried out in the Lake Biwa-Yodo River basin which provides multiple land uses and also the natural water resource for nearly 13 million of population in the region. Annual emissions for 214 nonmetallic compounds were calculated using the chemical emission data on Japanese pollutant release and transfer registry and used for executing the model simulations for 1997, 2002, and 2008 as input data. The calculated chemical concentrations by the model for all the environmental media were analyzed to determine trends in concentration over this study span. The majority of the chemicals decreased in concentration over time. Among the 214 nonmetallic chemical pollutants, 36 chemicals did not decrease in concentration and were in the top 10 % for concentration on average. Of these 36 pollutants, 7 occur in all 4 environmental media and pose a potential health risk at humans in the Lake Biwa-Yodo River basin.