Biological invasions pose a major threat to biodiversity, ecosystem functioning, and human well-being. Non-native species can have severe ecological impacts that are transformative, affecting ecosystems across both short-term and long-term timescales. However, few studies have determined the temporal dynamics of impact between these scales, impeding future predictions as invasion rates continue to rise. Our study uses a meta-analytical approach to dissect the changing taxonomic and functional impacts of biological invasions on native macroinvertebrate populations and communities in freshwater ecosystems across Europe, using a recently collated European long-term time series spanning several decades. Our findings reveal a complex temporal pattern: while initial stages of invasions (i.e. five years after the first record of non-native species) often exhibited benign impacts on macroinvertebrate abundance, richness, or functional diversity, the long-term (i.e. the period following the early invasion) effects became predominantly negative. This pattern was consistent between taxonomic and functional metrics for impacts at both the population and species level, with taxonomic metrics initially positively affected by invasions and functional metrics being more stable before also declining. These results suggest that even initially benign or positively perceived impacts could be eventually superseded by negative consequences. Therefore, understanding the magnitude of invasion effects increasingly requires long-term studies spanning several years or decades to offer insights into effective conservation strategies prioritising immediate and future biodiversity protection efforts. These findings also highlight the importance of integrating multiple taxonomic, functional and temporal components to inform adaptive management approaches to mitigate the negative effects of current and future biological invasions.