Introduction: Aquatic floodplain ecosystems along the Lower Danube are among most biodiverse freshwater habitats in Europe, yet they are increasingly affected by eutrophication, hydrological alteration and climate change. Long-Term Ecosystem Research (LTER) provides a framework for integrating biodiversity observations with environmental drivers across these ecosystems. Scope: The study aimed to assess the biodiversity and ecological status of aquatic ecosystems on two of the largest Danube floodpains - Brăila islands and Danube Delta, Romania. The objectives were to: characterize the qualitative and quantitative composition of phytoplankton, phytobenthos, macrophytes, zooplankton, and macrozoobenthos, and assess ecological status/potential using phytobenthos and macrophytes as biological quality elements. evaluate sensor-based versus microscopy-based monitoring methods for detection and assessment of the main algal groups. characterize the qualitative and quantitative composition of phytoplankton, phytobenthos, macrophytes, zooplankton, and macrozoobenthos, and assess ecological status/potential using phytobenthos and macrophytes as biological quality elements. evaluate sensor-based versus microscopy-based monitoring methods for detection and assessment of the main algal groups. Materials and Methods: Ecological monitoring was conducted in July 2025 at ten sites along the Lower Danube, including two Brăila Island lakes (Blasova and Zaton), two Danube sidearm stations along Brăila islands, three stations at Carasuhat Canal and three in Razim Lake. In situ measurements of temperature, dissolved oxygen, electrical conductivity, pH, as well as concentration of photosynthetic pigments like chlorophyll a , phycocyanin, and fluorescence-based algal group were measured using YSI EXO2 multiparameter probe and FluoroProbe BBE fluorometer. Five groups of organisms - phytoplankton, phytobenthos, zooplankton, macroinvertebrates, and macrophytes were sampled and taxonomically identified. Ecological status was assessed for phytobenthos (IPS/EQR) and macrophytes (AIM, RI/EQR) using national assessment methods for river type R6 and lake type L5. Phytoplankton abundance and biomass, as well as the richness and abundance of macroinvertebrate, zooplankton and macrophyte communities, were also determined. Results: Considerable differences in biodiversity and ecological status were observed among the investigated ecosystems. Phytoplankton richness reached 148 taxa (100 identified to species level): Cyanoprokaryota (35 taxa), Chlorophyta (72), Bacillariophyta (17), Cryptophyta (6), Euglenophyta (12), Chrysophyta (1), Pyrrhophyta (2), and Xanthophyta (3). Species diversity (Shannon index, H’) ranged from 1.59 at lake Blasova to 4.62 in the Danube Delta. Overall, 236 diatom taxa were identified, with nearly half exceeding 1% relative abundance in at least one of the samples. Most of the sites were dominated by halobious taxa, tolerant of higher salinity, particularly Lake Blasova, where marine-brackish species comprised approximately 90% of the diatom flora. The highest macrophyte diversity was recorded in Razim Lake, including the rare species Nuphar lutea and Trapa natans . The Danube sidearm stations were dominated by Vallisneria spiralis and Butomus umbellatus. Macroinvertebrates were most diverse (with more than 10 systematic groups) in Zaton and Blasova Lakes and the coastal part of Razim Lake, whereas the Danube sidearm upstream of Brăila and Carasuhat Canal supported less diverse communities dominated by molluscs, with bivalves prevailing at the river sites. Overall, 74 zooplankton taxa were identified, including 14 Crustacea (7 Cladocera and 7 Copepoda) and 60 Rotifera. Brachionus angularis was the dominant species in Brăila lakes, Brachionus forficula dominated Razim lake , while nauplii and copepodites co-dominated along with several Brachionus species in the Danube sites. The ecological status/potential based on phytobenthos ranged from bad (Lake Blasova and Carasuhat Canal) to poor (Carasuhat Site 2) and moderate (Danube, Razim Lake and Zaton Lake). The assessment based on macrophytes community classified Carasuhat Canal, Zaton Lake and Blasova Lake in bad ecological status/potential, while Razim Lake in moderate ecological status and Danube sidearm stations in moderate and good status. Fluorescence-based estimates of the major phytoplankton groups were comparable with conventional microscopy, with both methods generally identifying the same dominant groups, despite differences in the calculated contributions of cyanobacteria, green algae, and diatoms (PERMANOVA, p = 0.8616). Conclusion: The biodiversity and ecological condition of the investigated floodplain ecosystems differed, reflecting habitat heterogeneity and hydrological connectivity. Most sites exhibited poor to moderate ecological status despite their high biodiversity. The good comparability between fluorescence-based sensor measurements and conventional microscopic analyses indicates that sensor-based monitoring could provide a robust approach for long-term ecosystem assessment within the LTER framework.