To obtain a high rice yield and quality for animal feed without synthetic fertilizers, an experiment with bench-scale apparatus was conducted by applying continuous irrigation with treated municipal wastewater (TWW). Uniform rice seedlings of a high-yield variety (Oryza sativa L., cv. Bekoaoba) were transplanted in five treatments to examine different TWW irrigation directions (“bottom-to-top” and “top-to-top” irrigation) and fertilization practices (with and without P-synthetic fertilizers) as well as one control that simulated the irrigation and fertilization management of normal paddy fields. The highest rice yield (14.1 t ha−1), shoot dry mass (12.9 t ha−1), and protein content in brown rice (14.6%) were achieved using bottom-to-top irrigation, although synthetic fertilizers were not applied. In addition, this subsurface irrigation system could contribute to environmental protection by removing 85–90% of nitrogen from TWW more effectively than the top-to-top irrigation, which showed a removal efficiency of approximately 63%. No accumulation of heavy metals (Fe, Mn, Cu, Zn, Cd, Ni, Pb, Cr, and As) in the paddy soils was observed after TWW irrigation for five months, and the contents of these metals in the harvested brown rice were lower than the permissible limits recommended by international standards. A microbial fuel cell system (MFC) was installed in the cultivation system using graphite-felt electrodes to test the capacity of electricity generation; however, the electricity output was much lower than that reported in normal paddy fields. Bottom-to-top irrigation with TWW can be considered a potential practice to meet both water and nutrient demand for rice cultivation in order to achieve a very high yield and nutritional quality of cultivated rice without necessitating the application of synthetic fertilizers.