In the Sanjiang Plain, agricultural drainage ditches effectively alleviate agricultural non-point source nitrogen pollution. However, limited information is known about the characteristics of bidirectional trans-ports of nitrogen between sediment and overlying and pore water in different patterns of ditches undergoing seasonal freezing-thawing cycles. It is vital to better understand nitrogen interception and purification by ecological ditches. In order to clarify the interception of ecological ditches on internal and external nitrogen, overlying water and sediment samples of two typical agricultural ditches were collected and analyzed in Sanjiang Plain during the growing seasons of 2015–2017. The results indicated that the N-NO3− in overlying water, which was higher than N-NH4+, was the dominant inorganic nitrogen, whilst, in the sediment, N-NH4+ was much higher than N-NO3−, which should be attributed to the soil’s adsorption of N-NH4+. In contrast to the dryland ditch, the paddy ditch had a more significant amount of inorganic nitrogen both in overlying water and sediment, which means that the non-point source nitrogen pollution caused by paddy fields was more severe than that of drylands. Compared with dryland ditches, N-NH4+ in the sediment of pad ditches seemed to be much easier to migrate to a deeper layer, which may cause a greater risk of nitrogen pollution to groundwater. Both in the overlying water and the sediment of ditches, nitrogen content fluctuated during different periods, and inter-annual variation was noticeable, which results means that estimation or prediction of the non-point source pollution output needs to extend the monitoring period and increase sampling frequency to reduce the great uncertainty. The findings may provide a foundation for forecasting agricultural nitrogen pollution and guide best management practices (BMPs) of non-point source nitrogen pollution control in seasonally frozen areas.