The study of controlling the molecular self-assembly of aqueous soft matter is a fundamental scheme across multiple disciplines such as physics, chemistry, biology, and materials science. In this work, we use liquid-crystal polymer networks (LCNs) to control the superstructures of one aqueous soft material called lyotropic chromonic liquid crystals (LCLCs), which shows spontaneous orientational order by stacking the plank-like molecules into elongated aggregates. We synthesize a layer of patterned LCN films by a nematic liquid-crystal host in which the spatially varying molecular orientations are predesigned by plasmonic photopatterning. We demonstrate that the LCLC aggregates are oriented parallel to the polymer filaments of the LCN film. This patterned aqueous soft material shows immediate application for controlling the dynamics of swimming bacteria. The demonstrated control of the supramolecular assembly of aqueous soft matter by using a stimuli-responsive LCN film will find applications in designing dynamic advanced materials for bioengineering applications.