Nutrient emissions from paddy fields are one of the main sources of agricultural non-point source (NPS) pollution. Based on the “4R” (Reduce-Retain-Reuse-Restore) strategical system of agricultural NPS pollution control, ecological ditches are effective control measures under the “Retain” system. In this study, the nutrient removal efficiency and stoichiometric variations in three different ecological ditch systems were studied in order to better understand the long-term performance of ecological ditches, and to determine which type of ecological ditch system (Eh, concrete ecological ditch with holes on the wall; Ec, concrete ecological ditch; and Es, soil ecological ditch) is optimal for the removal of agricultural NPS pollutants. The results indicated that the converted ecological ditch (Eh type) significantly reduced nutrient levels in two-year rice season runoff compared to a traditional concrete ditch. The average removal efficiencies of total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) in the converted ecological ditch were 20.8 %, 37.0 %, and 44.4 %, respectively. All ecological ditch types had considerable capacity to remove nutrients in simulated rice season runoff. There were no significant differences in the efficiency of nutrient removal between Eh (TOC 24.1 %, TN 42.8 %, and TP 52.6 %) and Es (TOC 20.3 %, TN 35.7 %, and TP 47.9 %). However, the results indicated that Eh systems could provide a relatively stable environment for plants with increased capacity to maintain biological homeostasis. Of the three ditch types, Ec (TOC 12.9 %, TN 23.3 %, and TP 32.6 %) had a relatively low removal efficiency. Redundancy analysis (RDA) indicated that leaf P content, sediment C:N ratio and root N content were more closely related to water variables, and nutrient stoichiometric characteristics of water, plants, and sediment systems were significantly related to the nutrient removal capacity of ecological ditches (99.5 % of the total variation). It is anticipated that this study will promote further development of the “4R” strategical system, and encourage additional improvements to ecological ditches so they can become more effective in reducing agricultural NPS pollution in the field.