Freshwater ecosystems are important for global biodiversity and provide essential ecosystem services. There is consensus in the scientific literature that freshwater ecosystems are vulnerable to the impacts of environmental change, which may trigger irreversible regime shifts upon which biodiversity and ecosystem services may be lost. There are profound uncertainties regarding the management and assessment of the vulnerability of freshwater ecosystems to environmental change. Quantitative approaches are needed to reduce this uncertainty. We describe available statistical and modeling approaches along with case studies that demonstrate how resilience theory can be applied to aid decision-making in natural resources management. We highlight especially how long-term monitoring efforts combined with ecological theory can provide a novel nexus between ecological impact assessment and management, and the quantification of systemic vulnerability and thus the resilience of ecosystems to environmental change.