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In the presence of appropriate substrates, surface-anchored enzymes can act as pumps and propel fluid through microchambers. Understanding the dynamic interplay between catalytic reactions and fluid flow is vital to enhancing the accuracy and utility of flow technology. Through a combination of experimental observations and numerical modelling, we show that coupled enzyme pumps can exhibit flow enhancement, flow suppression, and changes in the directionality (reversal) of the fluid motion. The pumps’ ability to regulate the flow path is due to the reaction selectivity of the enzymes; the resultant fluid motion is only triggered by the presence of certain reactants. Hence, the reactants and the sequence in which they are present in the solution, and the layout of the enzyme-attached patches form an “instruction set” that guides the flowing solution to specific sites in the system. Such systems can operate as sensors that indicate concentrations of reactants through measurement of the trajectory along which the flow demonstrates maximal speed. The performed simulations suggest that the solutal buoyancy mechanism causes fluid motion and is responsible for all the observed effects. More broadly, our studies provide a new route for forming self-organizing flow systems that can yield fundamental insight into non-equilibrium, dynamical systems.