The dataset contains 16S rRNA gene amplicon sequencing data and corresponding metadata (hydrological and water quality parameters) for the Joint Danube Surveys 2 and 3 (JDS2 and JDS3), conducted in 2007 and 2013. Raw sequence data is available on the NCBI Sequence Read Archive (accession number SRP045083 for JDS2 and PRJNA835446 for JDS3). The current dataset contains: processed 16S rRNA gene amplicon sequencing data (rarefied ASV tables) corresponding taxonomy table metadata table The dataset covers three subsets: JDS2-PA, JDS2-FL and JDS3. During Joint Danube Survey 2, collected water samples were processed for two size fractions: > 3 µm fraction is considered to cover particle-associated microorganisms (JDS2-PA dataset), the 0.2 0.2 µm, JDS3 dataset). The metadata table contains the following parameters: Discharge - Discharge of the Danube River (m3/s) Flow - Flow velocity of the Danube River (m/s) travel_time_h - Water travel time (h), the time it took for the water to travel (flow) from the first sampling point. Calculated based on flow velocity and distance (river km) River_km area.1 - Catchment area [km2] 50 % - Median dendritic stream length [km], Dendritic stream length refers to the measurement of the distance along the channel of streams within a dendritic drainage basin, a common drainage pattern that resembles tree branches. The median dendritic stream length is the median length for a given stream order. Sum.of.subcatch.lengths - Cumulative dendritic stream lengths [km], the total length of all streams in the catchment. WaterTemperature (°C) pH Conductivity (µS/cm) DissolvedOxygen (mg/L) DOC - Dissolved organic carbon (mg/L) TotalSuspendedSolids (mg/L) Nitrate (mg/L) TotalPhosphorus (mg/L) OrthophosphatePhosphorus (mg/L) Phytoplankton_Biomass_Chla - Chlorophyll-a (µg/L) BNT_unfiltered - Total cell counts in the bulk sample (not fractionated) (cells/mL) Production_total - Bacterial secondary production [µgC L-1 h-1] lg_ecoli - the faecal indicator Escherichia coli (MPN/100mL), log10(x+1)-transformed ASV_richness_j2f - count of observed ASVs in JDS2-FL ASV_richness_j2p- count of observed ASVs in JDS2-PA ASV_richness_j3- count of observed ASVs in JDS3