Three different types of ditches, each 300 m in length, were employed in this study. One vegetated constructed ditch (VCD), three natural vegetated soil ditches (NVSD), and three constructed ditches left unvegetated (UCD) as controls were investigated using simple in/out mass balances and uptake by plant species with a potential for phytoremediation and their mechanisms. Significant differences in the ditches were observed, suggesting the importance of plant species in nutrient mitigation. The removal rates of TN (total nitrogen) and TP (total phosphorus) were 64.28 and 58.02, 31.16 and 27.49, and 3.91 and 2.97%, respectively, in the VCD, NVSD, and UCD. Canna indica (45.12 g m−2) and Oenanthe javanica (21.48 g m−2) had the highest total N and P storage in the VCD and NVSD. Furthermore, species C. indicapossessed the highest annual N and P uptake in the VCD (216.59 kg N/ha/yr and 30.73 kg P/ha/yr). In the NVSD, species O. javanica had the greatest annual N and P uptake (96.66 kg N/ha/yr and 7.94 kg P/ha/yr). Both VCD and NVSD were found to have a reasonably good outcome compared to UCD. Retention of nutrients by ditch sediments was probably the major attenuation mechanism, with subsequent plant uptake and microbial nitrification–denitrification of the nutrients as secondary removal mechanisms. Results of this study highlight the importance of taking actions for establishment of appropriate plant species inside the ditches in order to enhance its direct and indirect roles and maximize purification rate in aquatic environments.