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Due to the extensive application of artificial nitrogen-based fertilizers on land, groundwater from the central part of Taiwan faces problems of increasing concentrations of nitrate, which were measured to be well above 30 mg/L all year round. For meeting the 10 mg/L nitrate standard, optimal operations for a heterotrophic denitrification pilot plant designed for drinking water treatment was investigated. Ethanol and phosphate were added for bacteria growing on anthracite to convert nitrate to nitrogen gas. Results showed that presence of high dissolved oxygen (around 4 mg/L) in the source water did not have a significantly negative effect on nitrogen removal. When operated under a C/N ratio of 1.88, which was recommended in the literature, nitrate removal efficiency was measured to be around 70%, sometimes up to 90%. However, the reactor often underwent severe clogging problems. When operated under C/N ratio of 1.0, denitrification efficiency decreased significantly to 30%. Finally, when operated under C/N ratio of 1.5, the nitrate content of the influent was almost completely reduced at the first one-third part of the bioreactor with an overall removal efficiency of 89–91%. Another advantage for operating with a C/N ratio of 1.5 is that only one-third of the biosolids was produced compared to a C/N value of 1.88.