Aquatic ecosystems are almost invariably connected to other ecosystems because the dominant force of water movement facilitates physical, chemical, and biological exchanges among ecosystems. In this sense, we define an ecosystem linkage as any persistent or recurring process or attribute that connects different ecosystems in some manner. We argue that such linkages are integral, even defining, components of aquatic ecosystem structure and function, and therefore, should be evaluated in the course of ecological studies. J-NABS has made significant contributions to our understanding of such linkages. The percentage of all publications in J-NABS addressing some ecological linkage has approached 10% in recent years. Historically, emphasis was placed on upstream–downstream linkages in flowing waters, and theory (e.g., river continuum, nutrient spiraling) has evolved largely around this phenomenon. However, other linkages among ecosystems have received increased attention in the past 20 y. These linkages include surface–subsurface, lake–stream, river–floodplain, and, more recently, marine–freshwater. We contend that many ecological processes, including primary production, nutrient cycling, organic matter processing, and secondary production, are driven by such exchanges because of the donor-controlled nature of many aquatic ecosystems. Exchanges of materials from aquatic ecosystems to terrestrial systems, caused by flooding, nutrient translocation, or insect emergence, can be substantial. Movement of energy and nutrients from the ocean to freshwaters, such as in the migrations of anadromous fishes, also can be dramatic. Despite increasing evidence of the importance of such linkages, considerable impediments to research, such as journal specialization, lack of interdisciplinary study teams, and limited funding of sufficient duration for such research, exist. Such obstacles are surmountable if investigators continue to emphasize that aquatic ecology will be advanced by the study of such linkages, and that environmental problems are better understood and solved in the context of that knowledge.