Although surface water and groundwater are increasingly referred to as one resource, there remain environmental and ecosystem needs to study the 10 m to 1 km reach scale as one hydrologic system. Streams gain and lose water over a range of spatial and temporal scales. Large spatial scales (kilometers) have traditionally been recognized and studied as river-aquifer connections. Over the last 25 years hyporheic exchange flows (1–10 m) have been studied extensively. Often a transient storage model has been used to quantify the physical solute transport setting in which biogeochemical processes occur. At the longer 10 m to 1 km scale of stream reaches it is now clear that streams which gain water overall can coincidentally lose water to the subsurface. At this scale, the amounts of water transferred are not necessarily significant but the exchanges can, however, influence solute transport. The interpretation of seemingly straightforward questions about water, contaminant, and nutrient fluxes into and along a stream can be confounded by flow losses which are too small to be apparent in stream gauging and along flow paths too long to be detected in tracer experiments. We suggest basic hydrologic approaches, e.g., measurement of flow along the channel, surface and subsurface solute sampling, and routine measurements of the water table that, in our opinion, can be used to extend simple exchange concepts from the hyporheic exchange scale to a scale of stream-catchment connection.