Drainage water from paddy fields is of high nutrient loads, and agricultural drainage ditches have enhanced nutrients input into the downstream water and caused eutrophication and hypoxia of downstream aquatic systems. Nevertheless, the fate of total phosphorus (TP), total nitrogen (TN) and total organic carbon (C-org) in ditch sediments is still indeterminate due to lacking of investigation on sediment samples of the Sanjiang Plain, Northeast China. The current study examined the variation of TP, TN and C-org contents in a natural ditch, and two planted ditches with low and high water levels, respectively, in Sanjiang Plain. The results of this study showed that the variations of TN and C-org contents were significant at depth from 0 to 20 cm in the natural and planted ditch sediments (p<0.05). However, no significant difference existed in TP contents between the planted ditch sediment layers (p>0.05). TP contents were higher in sediments of the planted ditch with low water level than that of the planted ditch with high water level (at 0-10 cm). According to the contrastive ditch experiment, influence of water level on TN and C-org contents was not obvious (p<0.05). But TN and C-org contents were significantly lower in the high water level-planted ditch than that in the natural ditch (p<0.05). Nitrogen (N) and carbon (C) pools were larger in the natural ditch sediments than that in the planted ditch sediments. The surface ditch sediments (0-20 cm) released P during the rice growing season. Plant, water level and drying-wetting process were all the factors affecting the variations of TP, TN and C-org contents. It is necessary to improve ditch management to effectively mitigate nutrients input from agricultural runoff, and decrease the potential pollution in the downstream receiving waters.