Some of the largest climate changes on Earth are projected for high-latitude polar and subpolar environments in the coming decades (IPCC, 2014). A number of simultaneous socio-environmental perturbations are affecting Patagonia (41-55 • S), a vast and complex ecosystem whose economic and societal well-being depends on coastal resources (∼80% of people live near-shore; the coastal economy provides>40,000 jobs). In this new scenario, overlapping natural variability (interannual-seasonal dynamics) and human-induced environmental changes (global change) are major drivers influencing the marine food web structure and functions. Evidence of large environmental changes has been detected in the Patagonia marine system through (a) regional-scale, climatic-oceanographic coupled anomalous events, (b) interannual hydrological changes (decreasing pattern) in freshwater river inputs (watersheds into fjords), and (c) more frequent coastal and oceanic microbial outbreaks (Harmful Algal Blooms). Those changes have highly uncertain effects for the basic functionalities, structure, and feedback responses of coastal systems and their coupling with hydrological (e.g., river streamflow) or biogeochemical (e.g., biological carbon pump) processes. The northern Patagonian fjords system is hypothesized to act as an indicator of large-scale climate change given strong environmental variability. This, combined with regional climatic-oceanographic events (e.g., El Niño Southern Oscillation, Southern Annular Mode) and effects of local anthropogenic activities (e.g., nutrient fluxes from extensive aquaculture, land change due to forestry) may impact the chemical and physical properties of the surface water, destabilizing biological productivity and chemical coastal processes. The present synthesis, which gives the results of systemicsensitive chemical and biological variables, may be useful to managers and in preventing socio-environmental impacts from increasing natural and anthropogenic phenomena in Chile's southern coastal system.