Short-chain chlorinated paraffins (SCCPs) are an extremely complex group of industrial chemicals and found to be potential persistent organic pollutants (POPs), and thus have attracted extensive concern worldwide. In this study, influent, effluent, and sludge were collected from a large sewage treatment plant (STP) in Beijing, China. Water, sediment, and aquatic species were also collected from a recipient lake that receives effluents discharged from the STP. These samples were then analyzed to investigate the effect of STP effluent on distribution and trophic transfer of SCCPs in the local aquatic ecosystem. Concentrations of total SCCPs (ΣSCCPs) in lake water and surface sediments were found in the range 162-176 ng/L and 1.1-8.7 μg/g (dry weight, dw), respectively. Vertical concentration profiles of sediment cores showed ΣSCCPs decreased exponentially with increasing depth. Specific congener composition analysis in sediment layers indicated possible in situ biodegradation might be occurring. High bioaccumulation of SCCPs was observed in the sampled aquatic species. The bioaccumulation factor (BAF) generally increased with the number of chlorines in the SCCP congeners. A significantly positive correlation between lipid-normalized ΣSCCPs concentration and trophic levels (R(2) = 0.65, p < 0.05) indicate that SCCPs can biomagnify through the food chain in the effluent-receiving aquatic ecosystem.