Streams and lakes are nested within, and intimately connected with, the surrounding terrestrial landscape. However, these aquatic components of the catchment are commonly neglected and often not included in studies and management plans that focus on terrestrial ecosystems. Developing an improved understanding of biotic and abiotic connectivity across these ecosystems is key for the advancement of knowledge‐based management of natural ecosystems. Here, we take advantage of existing and extensive long‐term monitoring of the terrestrial food web in the Norwegian Arctic to propose how both new and existing freshwater monitoring can be integrated with terrestrial monitoring to develop a unifying design for adaptive monitoring of low‐Arctic catchments. Specifically, we suggest that relevant cross‐ecosystem linkages between freshwater and terrestrial ecosystems should be integrated in long‐term monitoring, and we outline the methods and timing for how to do this and use the aquatic systems as sentinels for detecting climate‐driven changes. While the plan we present here is tailored for the Norwegian low‐Arctic, it provides an approach that can be more broadly applied (or modified) to monitor many terrestrial–aquatic meta‐ecosystems subjected to impact of climate change around the world.