Units of complex systems—such as neurons in the brain or individuals in societies—must communicate efficiently to function properly: e.g., allowing electrochemical signals to travel quickly among functionally connected neuronal areas in the human brain, or allowing for fast navigation of humans and goods in complex transportation landscapes. The coexistence of different types of relationships among the units, entailing a multilayer representation in which types are considered as networks encoded by layers, plays an important role in the quality of information exchange among them. While altering the structure of such systems—e.g., by physically adding (or removing) units, connections, or layers—might be costly, coupling the dynamics of subset(s) of layers in a way that reduces the number of redundant diffusion pathways across the multilayer system, can potentially accelerate the overall information flow. To this aim, we introduce a framework for functional reducibility which allow us to enhance transport phenomena in multilayer systems by coupling layers together with respect to dynamics rather than structure. Mathematically, the optimal configuration is obtained by maximizing the deviation of system's entropy from the limit of free and noninteracting layers. Our results provide a transparent procedure to reduce diffusion time and optimize noncompact search processes in empirical multilayer systems, without the cost of altering the underlying structure.