Characterizing the temporal changes of biotic communities and disentangling the importance of their driving mechanisms are central themes in ecology and environmental management. Non-native species have multiple adverse impact on native communities and species. However, there is a dearth of information on how non-natives influence the long-term dynamics of native communities. In this study, we compared the role of non-native species alongside various local and regional factors in the long-term dynamics of stream fish assemblages in the catchment area of Lake Balaton, Hungary, the largest lake in Central-Europe. Although, we found no consistent trend in species re-ordering between native and non-native species, native fish assemblages indicated significantly lower temporal stability with increasing relative abundance of co-occurring non-natives. Structural equation modelling revealed that assemblage dynamic patterns were also determined by a habitat degradation gradient. Moreover, habitat degradation and the presence of fishponds increased the relative abundance of non-native species, further affecting native assemblages through indirect interactions. Fish assemblage dynamics showed also some degree of finer-scale spatial structure. Non-metric multidimensional scaling further reinforced the destabilizing effect of non-native species but highlighted that native fish assemblages could generally be described by non-directional gradual or saltatory changes over time, regardless of the relative abundance of non-natives. Our results thus revealed that the studied native fish assemblages may possess some degree of resilience against biological invasions. However, increasing temporal variability induced by non-natives makes native assemblages more vulnerable to environmental stochasticity threatening their long-term persistence. This is especially worrying, since the frequency and intensity of environmental disturbances are expected to rise in the future due to climate change and increasing anthropogenic pressure on aquatic ecosystems.

eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We carried out a 2850 km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a non-linear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65.106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results show a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.