Cities such as Flint, Michigan, and Milwaukee, Wisconsin serve as contemporary examples of how a lack of understanding of the environmental chemistry of freshwater reservoirs can render potable water engineering systems unsustainable for local residents. In many cities, green engineering functions to increase aesthetic appeal without a broader consideration for recovering ecosystem processes. Our objective was to evaluate the role of biodiversity in the environmental quality of freshwater by using an aquaponic system with Allium cepa as a simple model system. We hypothesized that plant growth and development, macroinvertebrate behavior, and water quality would be affected by changes in biological complexity. We further characterize how biological complexity in an aquaponic system impacts plant dynamics, macroinvertebrate behavior, and water quality. Our findings demonstrate how aquatic organisms can modify plant systems as well as water quality, and further suggest that biological complexity and diversity have the ability to ameliorate polluted water systems. We propose that green engineering infrastructure has the capacity to integrate and sustain ecosystem function recovery in urban contexts.