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Abstract While the disciplines of oceanography and limnology often operate in isolate, freshwater, estuarine, and marine ecosystems are intricately linked. The emphasis of this special issue for Limnology and Oceanography is on the aquatic continuum and the connectivity between aquatic ecosystems from headwater streams and inland waters, to coastal and marine systems. Changes in the transport and transformation of elements as well as ecological functions occur along this aquatic continuum. Assemblages of organisms change in a way that reflects the ecological and biogeochemical conditions of the aquatic gradient. Here, we highlight research progress in limnology and oceanography across the aquatic continuum and at the interfaces of headwaters to oceans. Contributions explored nutrient and carbon dynamics which included release, transportation, transformation, and stoichiometry from freshwaters to marine. The special issue also explored food web continua, including functional changes, biodiversity gradients, and photosynthesis and respiration comparisons among ecosystems at different points in the continuum. Rapid improvements in biomolecular techniques, use of long‐term datasets, applications of novel statistical methods, and improved upscaling methods can transform the way aquatic scientists are describing biological organisms and communities from freshwaters to oceans. One important conclusion is the recognition that anthropogenic activities such as invasive species and nutrient pollution trigger challenge the current concepts of aquatic continua including the river continuum concept, the land to ocean continuum, river to estuary systems, and the submarine groundwater discharge. Both limnologists and oceanographers have much to gain from exchanging information with one another, especially in light of global change.