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Agricultural nonpoint-source pollution (ANPSP) is a key cause of global environmental problems. However, the estimation of ANPSP, based on agricultural land use type, crop management, and attenuation of pollutants with distance, is lacking. Using the Mun River Basin as an example, this study established quantitative response relationships between subbasin flows and hydrological and water quality parameters. A good matching of the monitored sections and the control area based on flow relationships was achieved. By determining flow paths and flow distances, the overland and in-river transport attenuations of ANPSP were clarified. The overland and in-river transport and attenuation parameters were also quantified. The land use distribution and structure were further refined through crop management, which included crop types and crop rotation (monocropping or double cropping). Based on the above procedures, quantitative relationships among land use pattern, crop management, attenuation of pollutants with distance, and river water quality were established and used to construct six kinds of regression models. Among these models, the best modeling results were obtained when the parameters of water quality, land use structure, crop management, and soil nutrient attenuation were included. The modeling accuracy in the dry season increased from 0.398 to 0.881 when information about attenuation with distance and crop management was included. Similarly, the modeling accuracy in the wet season increased from 0.365 to 0.727. This study’s findings indicate that the constructed water quality model is effective and has significance for the quantitative determination of ANPSP.