The aim of this study is to reach the maximum percentage of dissolved oxygen removal from industrial raw water using microchannel. In this study, two continuous and batch systems were used for the deoxygenation of water. Nitrogen and natural gas were studied as deoxygenation agents for the evaluation of microchannel efficiency. For an accurate investigation of the issue, the Box–Behnken response surface method was utilized for experiment design and analysis of results. The parameters of temperature (T), gas/liquid flow ratio (G/l), and residence time (t) were the effective factors on the efficiency of the system. The temperature was set in the range of 80−120 °C, G/L in the range of 2–8 for both systems, and the residence time was 1–5 s for the continuous system and 120-480 s for the batch system. The maximum elimination percentage for nitrogen and natural gas were obtained to be 97.105 and 98.530 when experiments were carried out at the optimum conditions predicted by Design Expert software (T = 80 °C, G/L