The Magellanic Sub-Antarctic ecoregion (MSE) was covered by ice during the Last Glacial Maximum (21,000 years ago), with consecutive advance and retreat of ice masses since the Quaternary. Currently, this ecoregion supports a wide range of flora and fauna, with an important variety of endemic species present in the archipelagic region of fjords and channels of the MSE. However, anthropogenic climate change has accelerated global warming, exacerbating glacier melt in the last decade. In this study, we evaluated the effect of glacial melting on the ecophysiology of Macrocystis pyrifera, a brown macroalga that forms underwater forests and is considered a keystone species susceptible to environmental change. Tissue samples were collected from apical and basal fronds of young individuals from three M. pyrifera populations located in the Fjord of the Mountains (FMO) (51º10'53"S, 73º17'08"W) and measurements of electron transport efficiency (Alpha), maximum relative rate of electron transport (rETRmax), saturation point (Ek), chlorophyll-a (Chl-a), chlorophyll-c (Chl-c), and fucoxanthin (Fucox) performed. Significant differences in photosynthetic response between apical and basal fronds were detected in populations directly affected by glacier melt relative to the population not influenced by glacial melt. Apical fronds exhibited better acclimatization to high light, turbidity, and temperature variations, while basal fronds demonstrated acclimatization to low irradiance levels, resulting in high rETRmax responses. Significant differences were detected in pigment concentrations at the site without glacier influence between apical and basal fronds. Our findings indicate that M. pyrifera employs a photo-acclimation strategy in fronds to mitigate physiological susceptibility to extreme environmental conditions.