The non-treated wastewater from residential areas contains high concentration of ammonium-nitrogen (NH4+-N). When discharged into the drainage water system, it deteriorates the water quality in urban rivers. This study used two types of materials to form eco-bags, using activated zeolite bead (AZB) and alkaline pretreated straw (APS), in geotextile bags for easy recovery and reuse. The AZB and APS provided the breeding habitat for the microorganisms that promoted biofilm formation on their surface. The immobilization of engineered denitrification microorganisms facilitated the removal of NH4+-N from the urban river water. The NH4+-N removal in the AZB and APS bags were in the range of 64–73%, and 56–61%, respectively, while the chemical oxygen demand (COD) removal in the AZB and APS bags ranged from 33–36%, and 30–31%, respectively. Besides, as evident from DNA and microbial community analysis, the microorganisms demonstrated a greater proclivity to grow and proliferate on the surface of AZB and APS and improved the water quality of urban rivers.