Danube Delta shallow lakes experience cyanobacteria blooms that can negatively affect the aquatic ecosystem. Although there are several studies on Danube Delta cyanobacteria, little is known about their spatial-temporal patterns and the potential predictive role they can offer.We therefore analyzed the distribution of cyanobacteria in 19 lakes belonging to three lake complexes, and tested whether their seasonal dynamics are in line with the predictions of the PEG model. Furthermore, we investigated to which extent cyanobacteria diversity and abundance were related to lake hydrogeomorphological characteristics such as: surface, water level, connectivity, water retention, flood risk, transparency. Although lakes had different seasonal cyanobacterial assemblages, the biovolume and genus richness had a geographical pattern, decreasing from south-east (lakes forming the fluvial delta) towards north-west (lakes forming the maritime delta). Cyanobacteria biovolume reflected largely the PEG model peaking in summer (the fluvial delta) and autumn ( the maritime delta). Genus richness followed the same pattern. Cyanobacteria distribution was predicted by various abiotic (e.g. risk of flooding, connectivity) and biotic factors (e.g. submersed macrophytes, phytoplankton diversity, peat deposits). Our study contributes to the understanding of cyanobacteria diversity and distribution in shallow interconnected lakes by revealing the complexity of predictors for geographical and seasonal patterns.