As the common features of agroecosystems, ditches and ponds benefit the irrigation and drainage, as well as intercepting non-point source pollutants. However, most ditch-pond studies have been conducted in lowland areas. To test this source-sink assumption in upland areas, this study made observations on the ecological function of the ditch and pond system in a typical catchment in China. First, the changes in ponds in the catchment were analyzed using high-resolution remote sensing data. Then, the migration of agricultural pollutants in ditches and ponds were analyzed by field sampling and laboratory detection. The results showed that over the past 15 years the length of ditches in the catchment and the number of small ponds (< 500 m²) have increased by 32% and 75%, respectively. The rate of change in nutrient concentrations in the ditches and ponds were mostly from −20% to 20%, indicating ditches and ponds can be both sources and sinks for agricultural pollutants. Lastly, the contributing factors were explored and it was found that ditches and ponds are important sinks in dry season. However, during the rainy season, ditches and ponds become sources of pollutants, with the rapid drainage of ditches and the overflow of ponds in upland areas. The results of this study revealed that the ditches and ponds could be used for ecological engineering in upland catchments to balance drainage and intercept pollutants.