Coastal upwelling systems off the coasts of Peru and Chile are among the most productive marine ecosystems in the world, sustaining a significant percentage of global primary production and fishery yields. Seasonal and interannual variability in these systems has been relatively well documented; however, an understanding of recent trends and the influence of climate change on marine processes such as surface cooling and primary productivity is limited. This study presents evidence that winds favorable to upwelling have increased within the southern boundary of the Humboldt Current System (35°–42°S) in recent decades. This trend is consistent with a poleward movement of the influence of the Southeast Pacific Anticyclone and resembles the spatial pattern projected by Global Circulation Models for warming scenarios. Chlorophyll a levels (from 2002 to present) determined by satellite and field-based time-series observations show a positive trend, mainly in austral spring–summer (December–January–February), potentially explained by observed increments in nutrient flux towards surface waters and photosynthetically active radiation. Both parameters appear to respond to alongshore wind stress and cloud cover in the latitudinal range of 35°S to 42°S. In addition, net annual deepening of the mixed layer depth is estimated using density and temperature profiles. Changes in this depth are associated with increasing winds and may explain cooler, more saline, and more productive surface waters, with the latter potentially causing fluctuations in dissolved oxygen and other gases, such as nitrous oxide, sensitive to changes in oxygenation. We argue that these recent changes represent, at least in part, a regional manifestation of the Anthropocene along the Chilean coast.