A challenge to managing water resources is characterizing the scale-dependent heterogeneity created by the interactions among hydrological, ecological and anthropological processes. It is often difficult to collect sufficient empirical data over the range of scales required to construct mathematical models that facilitate robust bottom-up descriptions or predictions. An alternative is identifying emergent properties of complex systems, whose components self-organize into novel structures or processes via their collective interactions with each other and the environment. A new level of organization and complexity emerges that cannot be predicted from or attributed to the components alone. Emergence offers a number of perspectives from which to interpret, if not predict, the behavior of complex water resource systems. One of these is entropy, which maximizes the options for system components to alter their interactions and, thus, permits variability and adaptability. At the scale of watersheds, increased entropy is pertinent because of its relationship to information (as probability functions), which is transmitted through connected components of a watershed in a manner such that the accrued information gives rise to emergent properties. Hence, analyzing the behaviors of a system according to emergence introduces the possibility of evaluating the information content via its interconnected components. Connectivity then assumes an integral role in a hydrologic system’s response to natural or anthropogenic disturbances (e.g., climate change, land use). Replacing the details of multi-scale heterogeneity and causal mechanisms with the functions that watersheds perform allows processes such as stream flow rate/duration and flood frequency to be construed as emergent spatiotemporal patterns. A reductionist or bottom-up approach to assessing the behavior of aquatic systems shifts to a functional or top-down approach that does not depend upon an understanding of all the physical, chemical or biological mechanisms involved. This latter approach could supplement conventional water resource descriptions and predictions via more comprehensively characterizing watershed or aquatic ecosystem functions.