This study set up two flow-through pilot-scale constructed wetlands with the same size but various flow patterns (free water surface flow (FWS) and subsurface flow (SSF)) to receive a nitrate-contaminated groundwater. The effects of hydraulic loading rate (HLR) on nitrate removal as well as the difference in performance between the various types of wetlands were investigated. Nitrate removal rates of both wetlands increased with increasing HLR until a maximum value was reached. The maximum removal rates, occurred at HLR of 0.12 and 0.07 m d−1, were 0.910 and 1.161 g N m−2 d−1 for the FWS and SSF wetland, respectively. After the maximum values were reached, further increasing HLR led to a considerable decrease in nitrate removal rate. Nitrate removal efficiencies remained high (>85%) and effluent nitrate concentrations always satisfied drinking water standard (<10 mg NO3–N L−1) when HLR did not exceed 0.04 m d−1 for both FWS and SSF wetlands. The first-order nitrate removal rate constant tends to decrease with increasing HLRs. The FWS wetland provided significantly higher (p < 0.05) organic carbon in effluent than the SSF wetland, while the SSF wetland exhibited significantly (p < 0.05) lower effluent DO than the FWS wetland. However, there was no significant difference (p > 0.05) in nitrate removal performance between the two types of constructed wetlands in this study except in one trial operating at HLR of 0.06–0.07 m d−1.