Hydrological connectivity regulates water residence, resource availability and dispersal across freshwater networks, but its links with microbial community organisation remain difficult to resolve in spatially complex deltaic systems. We combined stable water isotopes, hydrochemistry and 16S rRNA gene amplicon sequencing to examine bacterioplankton turnover across riverine, channel and lake habitats in the Danube Delta. Twenty sites were sampled in September 2023. Surface-water δ¹⁸O–δ²H values defined a coherent evaporation line (slope = 5.22, R² = 0.981), ranging from isotopically depleted river waters to enriched lake waters and indicating increasing evaporative influence and effective hydrological retention. Alpha-diversity metrics did not differ significantly among habitats, whereas Bray–Curtis dissimilarities revealed pronounced community turnover along the river–lake continuum. The primary axis of bacterioplankton variation was strongly associated with δ¹⁸O enrichment, linking microbial community organisation to independently resolved water history. Verrucomicrobiota increased towards isotopically enriched, DOC-rich lake waters, whereas Proteobacteria and Actinobacteriota were associated with more connected riverine conditions. A redundancy analysis constrained by DOC, conductivity, total nitrogen and total phosphorus explained 50.3 % of Hellinger-transformed phylum-level variation. Together, these results show that hydrological connectivity and water history are closely coupled to microbial community reorganisation and associated carbon and nutrient conditions across a heterogeneous deltaic network. Stable water isotopes therefore provide a process-based hydrological context for interpreting bacterioplankton turnover in freshwater landscapes.