Rivers are conduits for materials and energy; this, the frequent and intense disturbances that these systems experience, and their narrow, linear nature, create problems for conservation of biodiversity and ecosystem functioning in the face of increasing human influence. In most parts of the world, riparian zones are highly modified. Changes caused by alien plants — or environmental changes that facilitate shifts in dominance creating novel ecosystems — are often important agents of perturbation in these systems. Many restoration projects are underway. Objective frameworks based on an understanding of biogeographical processes at different spatial scales (reach, segment, catchment), the specific relationships between invasive plants and resilience and ecosystem functioning, and realistic endpoints are needed to guide sustainable restoration initiatives. This paper examines the biogeography and the determinants of composition and structure of riparian vegetation in temperate and subtropical regions and conceptualizes the components of resilience in these systems. We consider changes to structure and functioning caused by, or associated with, alien plant invasions, in particular those that lead to breached abiotic- or biotic thresholds. These pose challenges when formulating restoration programmes. Pervasive and escalating human-mediated changes to multiple factors and at a range of scales in riparian environments demand innovative and pragmatic approaches to restoration. The application of a new framework accommodating such complexity is demonstrated with reference to a hypothetical riparian ecosystem under three scenarios: (1) system unaffected by invasive plants; (2) system initially uninvaded, but with flood-generated incursion of alien plants and escalating invasion-driven alteration; and (3) system affected by both invasions and engineering interventions. The scheme has been used to derive a decision-making framework for restoring riparian zones in South Africa and could guide similar initiatives in other parts of the world.