Trophic interactions can result in changes to the abundance and distribution of habitat-forming species that dramatically reduce ecosystem functioning. In the coastal zone of the Aleutian Archipelago, overgrazing by herbivorous sea urchins that began in the 1990s resulted in widespread deforestation of the region's kelp forests, which led to lower macroalgal abundances and higher benthic irradiances. We examined how this deforestation impacted ecosystem function by comparing patterns of net ecosystem production (NEP), gross primary production (GPP), ecosystem respiration (Re), and the range between GPP and Re in remnant kelp forests, urchin barrens, and habitats that were in transition between the two habitat types at nine islands that spanned more than 1000 kilometers of the archipelago. Our results show that deforestation, on average, resulted in a 24% reduction in GPP, a 26% reduction in Re, and a 24% reduction in the range between GPP and Re. Further, the transition habitats were intermediate to the kelp forests and urchin barrens for these metrics. These opposing metabolic processes remained in balance; however, which resulted in little-to-no changes to NEP. These effects of deforestation on ecosystem productivity, however, were highly variable between years and among the study islands. In light of the worldwide declines in kelp forests observed in recent decades, our findings suggest that marine deforestation profoundly affects how coastal ecosystems function.of the region's river systems and its riparian plant communities [4,5]. Similarly, large marine algae, such as kelps, can form subtidal forests whose biogenic structures alter hydrodynamic, nutrient and light conditions, modify patterns of biodiversity, enhance primary production and carbon sequestration, and provide food and habitat for numerous other species [6][7][8][9]. Consequently, the loss of these forest-forming kelps and the benthic communities they support can have dramatic impacts to how nearshore ecosystems function, especially if they occur over large geographic areas. Indeed, kelp deforestation has occurred in numerous areas worldwide in recent decades due to a variety of forcing factors [10,11], and the subtidal rocky reefs of the Aleutian Archipelago serve as a model system to investigate the broader impacts of such deforestation. These forests have historically been dominated by dense populations of the surface canopy-forming kelp Eualaria fistulosa, several species of understory kelps such as Laminaria spp. and Agarum spp., the brown alga Desmarestia spp., and numerous species of fleshy read algae. However, the collapse of sea otter (Enhydra lutris) populations led to large increases in their primary prey, herbivorous sea urchins (Strongylocentrotus polyacanthus), which subsequently resulted in overgrazing and widespread losses of the region's kelp forests [12]. This collapse began in the late 1990s, likely in response to a dietary shift by killer whales toward sea otters, and by 2000 sea otter densities had declined throughout the ar...