A cooperatively coupled, isothermal biochemical amplification system has been investigated under flow conditions in a microstructured reactor. The experimental setup provides for continuous amplification and on line detection of the reaction products in space and time. Spatially resolved fluorescence spectroscopy with an intercalating dye was used for detection of the double stranded DNA products. Biochemical amplification was observed under a wide range of flow rates. The total rate of amplification resulted from an interplay between the amplification of the biochemical system and a loss term produced by the flow. For flow rates above a critical value, the system was diluted out and the amplification reaction brought to a halt in the reactor. Homogeneous growth throughout the reactor was observed at intermediate flow rates. At low pump rates, additional biochemical amplification started at various locations. We interpret the spatially homogeneous Growth at low concentration and the local growth at high concentration to result from two different amplification phases because of noncooperative and cooperative amplification mechanisms, respectively. The consequences for long-term evolutionary experiments as well as for complex pattern formation are discussed.