Freshwater inputs strongly influence oceanographic conditions in coastal systems of northwestern Patagonia (41–45°S). Nevertheless, the influence of freshwater on these systems has weakened in recent decades due to a marked decrease in precipitation. Here we evaluate potential influences of climate and land cover trends on the Puelo River (640 m3s–1), the main source of freshwater input of the Reloncaví Fjord (41.5°S). Water quality was analyzed along the Puelo River basin (six sampling points) and at the discharge site in the Reloncaví Fjord (1, 8, and 25 m depth), through six field campaigns carried out under contrasting streamflow scenarios. We also used several indicators of hydrological alteration, and cross-wavelet transform and coherence analyses to evaluate the association between the Puelo River streamflow and precipitation (1950–2019). Lastly, using the WEAP hydrological model, land cover maps (2001–2016) and burned area reconstructions (1985–2019), we simulated future land cover impacts (2030) on the hydrological processes of the Puelo River. Total Nitrogen and total phosphorus, dissolved carbon, and dissolved iron concentrations measured in the river were 3–15 times lower than those in the fjord. Multivariate analyses showed that streamflow drives the carbon composition in the river. High streamflow conditions contribute with humic and colored materials, while low streamflow conditions corresponded to higher arrival of protein-like materials from the basin. The Puelo River streamflow showed significant trends in magnitude (lower streamflow in summer and autumn), duration (minimum annual streamflow), timing (more floods in spring), and frequency (fewer prolonged floods). The land cover change (LCC) analysis indicated that more than 90% of the basin area maintained its land cover, and that the main changes were attributed to recent large wildfires. Considering these land cover trends, the hydrological simulations project a slight increase in the Puelo River streamflow mainly due to a decrease in evapotranspiration. According to previous simulations, these projections present a direction opposite to the trends forced by climate change. The combined effect of reduction in freshwater input to fiords and potential decline in water quality highlights the need for more robust data and robust analysis of the influence of climate and LCC on this river-fjord complex of northwestern Patagonia.