Dynamic control of protein transport across hydrogel membranes can be achieved through modulation of electrical forces to (1) directly alter solute flux, and (2) alter membrane microstructure. Potential applications include separation processes and controlled drug delivery. In this study, transmembrane electric fields and changes in the composition of the electrolyte bath enable selective control of the transport of fluorescently labelled proteins and neutral solutes across polymethacrylic acid and polyacrylamide membranes. Four distinct mechanisms for controlling solute flux are identified: electromechanical deformation of the membrane, electroosmotic and electrophoretic augmentation of solute flux within the membrane, and electrostatic partitioning of charged solutes into charged membranes. Results of experiments involving separation of two solutes demonstrate that changes in solute flux depend on both solute size and charge. By optimizing membrane composition and operating conditions for solutes of interest, large solute-selective changes in permeability can be controlled through a combination of the above mechanisms.