Most freshwater systems are interconnected, whether through river drainage networks, as chains of lakes, or through groundwater movement. At the SFS meeting in San Juan, we emphasize the coupling of upland and lowland systems in our choice of special sessions and contributed papers. Consideration of entire networks of inland aquatic systems from mountains to estuaries and the sea has been made more feasible by advances in remote sensing, water quality sensors, and modeling approaches. Yet intermittent disconnection of aquatic systems as well as extensive flooding is becoming more common due to the increased frequency of extreme events due to climate change. Both extremes pose significant challenges to our understanding of the networking of inland aquatic systems and their connections to coastal ecosystems.