Climate change is altering biodiversity, but the relative influence of short-term weather variability and long-term climate trends on species and functional diversity remains unclear. While predictive models suggest functional homogenisation, empirical assessments of functional diversity variation using standardized abundance data over longer temporal horizons and at regional scales remain scarce. In this study, we use a long-term dataset on bird communities in the Wadden Sea to investigate how functional diversity responds to climate and weather changes in island systems. We analysed 25 years of systematically collected abundance monitoring data on breeding and migrating birds on six barrier islands of the German Wadden Sea. While species diversity increased over time, functional diversity showed a decreasing trend across islands, indicating functional homogenisation. Breeding and migrating birds responded differently: breeding birds were mainly influenced by short-term weather fluctuations, while migrating birds responded more to long-term climate trends. Island size was an important predictor of functional diversity, with larger islands serving as refugia for functionally unique species. Our results provide empirical evidence to support and refine theoretical expectations of climate-induced changes in biodiversity. By integrating spatial and temporal perspectives, we show that biodiversity responses depend on species’ ecology and island characteristics. The observed effects highlight that biodiversity changes in response to climate change are more complex than expected from simple predictive models. Understanding these dynamics is important for predicting future biodiversity patterns and ecosystem resilience in a rapidly changing world.