This survey reports the spatial distribution of gastropods belonging to Caenogastropoda, Architaenioglossa, Littorinimorpha, Cycloneritida and Hygrophila orders, and malacostracans from Amphipoda and Mysida orders in the lower sector of the Danube River, Romania, using DNA barcoding based on the cytochrome C oxidase I (COI) gene sequence. Sampling was performed for eight locations of Danube Delta branches and Bechet area during three consecutive years (2019–2021). Molecular identification of sixteen gastropods and twelve crustacean individuals was confirmed to the species level, providing the first molecular identification of gastropods from the Lower Danube sector. Phylogenetic analysis showed that species of gastropods and crustaceans clustered in monophyletic groups. Among gastropods, Microcolpia daudebartii acicularis, Viviparus viviparus, Bithynia tentaculata, Physa fontinalis, Ampullaceana lagotis and Planorbarius corneus were identified in Chilia and Sulina branches; and the Bechet area was populated by Holandriana holandrii, Theodoxus transversalis and Gyraulus parvus. The amphipods and mysids were present along the three main Danube branches. The calculated density of these species revealed an abundant community of crustacean Chelicorophium robustum on Sulina branch, and Dikerogammarus haemobaphes and D. villosus in extended areas of the Danube Delta. The presence of these invertebrates along Danube River was reported in relation to the sediment type and water depth.