Riverine habitats are vulnerable to a host of environmental stressors, many of which are increasing in frequency and intensity across the globe. Climate change is arguably the greatest threat on the horizon, with serious implications for freshwater food webs via alterations in thermal regimes, resource quality and availability, and hydrology. This will induce radical restructuring of many food webs, by altering the identity of nodes, the strength and patterning of interactions and consequently the dynamics and architecture of the trophic network as a whole. Although such effects are likely to be apparent globally, they are predicted to be especially rapid and dramatic in high altitude and latitude ecosystems, which represent ‘sentinel systems’. The complex and subtle connections between members of a food web and potential synergistic interactions with other environmental stressors can lead to seemingly counterintuitive responses to perturbations that cannot be predicted from the traditional focus of studying individual species in isolation. In this review, we highlight the need for developing new network-based approaches to understand and predict the consequences of global change in running waters.