Black-odorous waters are an increasingly common phenomenon characterized by excessive levels of nutrients, the formation of metal sufide precipitates, volatile sulfurous compounds, low dissolved oxygen and high chemical oxygen demand. Black-odorous waters frequently occur in lake and river systems where inputs have restricted circulation. The key remediation issue is the removal of nitrogen and phosphorus. Here, we present a novel aeration-adsorption system using fiber balls and we study treatment parameters and removal mechanism. Kinetics and changes of the solid phase were followed using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. Results show complete removal of ammonia N, initially at 31 mg/L, and 92.8% removal of total nitrogen, initially at 29 mg/L, after a 24 h reaction time at pH 9.67. At pH 5.67 and 9.67, total phosphorus and phosphate could be significantly reduced by 90–92% at 3.2–5.2 mg/L after 24 h. Treatment met China’s integrated wastewater discharge standards, demonstrating an effective and robust treatment capability. First-order and second-order kinetic models provided a good fit to the treatment data, indicating physical and chemical adsorption were involved in the treatment reactions. The reaction mechanism involved hydrogen substitution and binding to oxygen. These results present a cost effective and robust approach for the removal of N and P from black, odorous water, providing opportunity to abate environmental contamination.