Control of organic matter, nutrients and disinfection byproduct formation is a major challenge for the drinking water treatment plants on Matsu Islands, Taiwan, receiving source water from the eutrophic reservoirs. A pilot entrapped biomass reactor (EBR) system was installed as the pretreatment process to reduce organic and nitrogen contents into the drinking water treatment plant. The effects of hydraulic retention time (HRT) and combination of preceding physical treatment (ultraviolet and ultrasound) on the treatment performance were further evaluated. The results showed that the EBR system achieved higher than 81%, 35%, 12% and 46% of reduction in chlorophyll a (Chl a), total COD (TCOD), dissolved organic carbon (DOC) and total nitrogen (TN), respectively under varied influent concentrations. The treatment performance was not significantly influenced by HRT and presence/absence of physical pretreatment and the effluent water quality was stable; however, removal efficiencies and removal rates of Chl a, TCOD and DOC showed strong correlation with their influent concentrations. Excitation-emission matrix (EEM) fluorescence spectroscopy identified fulvic-like and humic-like substances as the two major components of dissolved organic matter (DOM) in the reservoir, and decreased intensity of the major peaks in effluent EEM fluorescence spectra suggested the effective removal of DOM without production of additional amount of soluble microbial products in the EBR. Through the treatment by EBR, about 10% of reduction of total trihalomethane formation potential for the effluent could also be achieved. Therefore, the overall results of this study demonstrate that EBR can be a potential pretreatment process for drinking water treatment plants receiving eutrophic source water.