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River monitoring and predicting analysis for establishing pollutant loads management require numerous budgets and human resources. However, it is general that the number of government officials in charge of these tasks is few. Although the government has been commissioning a study related to river management to experts, it has been inevitable to avoid the consumption of a massive budget because the characteristics of pollutant loads present various patterns according to topographic of the watershed, such as topology like South Korea. To address this, previous studies have used conceptual and empirical models and have recently used artificial neural network models. The conceptual model has a shortcoming in which it required massive data and has vexatious that has to enforce the sensitivity and uncertain analysis. The empirical model and artificial neural network (ANN) need lower data than a conceptual model; however, these models have a flaw that could not reflect the topographical characteristic. To this end, this study has used a convolution neural network (CNN), one of the deep learning algorithms, to reflect the topographical characteristic and had estimated the pollutant loads of ungauged watersheds. The estimation results for the biochemical oxygen demand (BOD) and total phosphorus (TP) loads for three ungauged watersheds were all excellent. However, prediction results with low accuracy were obtained when the hydrological images of a watershed with a land cover status different from the ungauged watersheds were used as training data for the CNN model.