This computational study investigates the sensing and actuating behavior of a pH-sensitive hydrogel-based microfluidic flow controller. This hydrogel-based flow controller has inherent advantage in its unique stimuli-sensitive properties, removing the need for an external power supply. The predicted swelling behavior the hydrogel is validated with steady-state and transient experiments. We then demonstrate how the model is implemented to study the sensing and actuating behavior of hydrogels for different microfluidic flow channel/hydrogel configurations: e.g., for flow in a T-junction with single and multiple hydrogels. In short, the results suggest that the response of the hydrogel-based flow controller is slow. Therefore, two strategies to improve the response rate of the hydrogels are proposed and demonstrated. Finally, we highlight that the model can be extended to include other stimuli-responsive hydrogels such as thermo-, electric-, and glucose-sensitive hydrogels.