Human activities are reshaping biodiversity in unprecedented ways. This reorganization has profound consequences on species interaction networks, like food webs that support ecological and evolutionary processes essential for life on Earth, prompting calls for including food webs in conservation planning. Yet, we still know little about the direction and magnitude of food web changes, especially at large spatial scales. Early work predicted that global environmental change would cause systematic loss of species and an overall homogenization of biological communities, leading to simplified food webs dominated by generalist species and their interactions. However, recent studies have shown that biodiversity responses in the Anthropocene are complex and suggested that different regions of the globe will experience greater or lower rates of change depending on the biogeographical context and the strength of human pressures. Combining extensive datasets of assemblage time-series, trophic interactions, and species traits, we reconstructed a global database of food web time-series in aquatic ecosystems to identify temporal and spatial patterns of changes in the structure and functioning of food webs across the globe. We inferred more than 15,000 food web time-series distributed in both freshwater and marine environments. he analysis of these time series showed that Global Environmental Change also affects other facets of biodiversity beyond population and community diversity changes. Despite the high variability we observed in the global trends, the response of food webs is spatially structured, with different rates of changes according to the biogeographic regions and environmental realms. Our results highlight that exploring other facets of biodiversity, like species interaction networks, is crucial to better understanding the current reshaping of biodiversity.