Rainwater is a source of freshwater that affects the aquatic and terrestrial ecosystems, and consequently human health. Since potential toxic elements (PTEs) have been found in rainwater in Southern Europe, its quality should be evaluated. This review assesses the current knowledge of the quality of rainwater in Southern Europe concerning PTEs, as well as its impact on the environment and human health. The presence of PTEs in rainwater poses challenges and simultaneously an opportunity for innovation in environmental management, particularly in water management. Further monitoring of rainwater quality, research, and policy development are needed to ensure that rainwater remains a viable and safe water resource. The challenges of rainwater quality regarding PTEs and of rainwater harvesting as a measure of drought mitigation, as observed in Southern Europe, require investing in rainwater treatment technologies. The treatment of rainwater harvested in Southern Europe can reduce environmental and health risks posed by PTEs, while enhancing the region’s resilience to climate change and water scarcity.