Imidacloprid pesticide is commonly used in the agricultural sector to protect from pest attacks and avoid crop losses. However, the leak of Imidacloprid to the environmental system could result in dire consequences to the aquatic life and humans as the toxic contaminant produced by this pesticide may disturb the ecosystem through the pesticide cycle, which could penetrate the soil and pollute the water body especially runoff. Therefore, this paper explains the new implementation in managing pesticide pollution that occurred in the agricultural runoff, specifically Imidacloprid pesticide. The assessment was conducted by introducing a treatment train system that focuses on a few removal mechanisms. The system included a series of bioretention columns that are expected to remove Imidacloprid through infiltration, plant uptake, and pesticide degradation. The system was also designed to have different configurations in order to analyze whether various additives and plants may affect the ability of treatment train in removing Imidacloprid. Hibiscus and Ti plants were used in the bioretention columns, while coconut husk and rice husk ash were used as additives. In addition, Imidacloprid that was present in all samples was analyzed using High-Performance Liquid Chromatography-Ultraviolet (HPLC-UV). The removal efficiency for every configuration was recorded based on Imidacloprid concentration in influent and effluent at every column in the treatment train system. The results indicated that the vegetation set achieved 90% of Imidacloprid removal efficiency while the control set (only soil media) removed Imidacloprid at a range between 64.9 to 65.9%. Furthermore, the vegetation set with additives also resulted in the increment of Dissolved Oxygen (DO) with about 16% and pH increment between 2 to 11% for all treatment train sets with a better water quality improvement.