The biological slow filtration (BSF) system as a simple and efficient environmental technology has been widely applied in treatment of ‘micro-polluted’ water. At present, many related studies have focused on the removal efficiency of biological indicators (such as bacteria and viruses). However, there is less research on the removal performance of nutrients and organics in the BSF system. In this paper, we employed a lab-scale biological slow filter to study the removal efficiency and degradation mechanism of nutrients and organics. We proved through adsorption of filter layer at the early running stage and biodegradation at the later stage, the BSF system could achieve effective removal of NH₃-N, TN, TP, CODMn and turbidity and the corresponding removal rates are 83.65%, 42.45%, 42.94%, 60.41% and 83.55%, respectively. Furthermore, we also explored the influence of four main factors (filtration rate, filter depth, hydraulic head and temperature) and their interactions on removal rates of nutrients and organics in the BSF system and obtained the optimal operating parameters as follows: filtration rate 0.1 m/h, filter depth 0.8 m, hydraulic head 0.64 m, temperature 26.06 °C. This study would provide a theoretical foundation for the actual application of biological slow filter in treatment of micro-polluted water in developing countries and offer an optimized basis for the design of operating conditions.