Active fluids have potential applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally varying activities. Ultraviolet light–activated caged ATP and fluorescent dyes were used to activate controlled regions of microtubule-kinesin active fluid, creating a binary active-inactive fluid where the progression of mixing was observed. At low flow-speed levels, mixing was governed by active fluid-induced diffusion-like processes at the active-inactive interface, but at higher flow-speed levels, mixing was governed by active fluid-induced superdiffusion-like processes. Samples activated in a checkerboard pattern reached homogeneity faster than those that were activated only on one side. A model of active nematohydrodynamics coupled to ATP transport was used to describe the coupled mixing process. The results show that the mixing of active fluid systems with initially nonuniform activities is governed by the complex active transport of ATP at the interface between active and inactive regions.