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The ecological status of Pampean shallow lakes is evidenced by Cyanobacteria Harmful Blooms impairing these nutrient enriched, turbid and polymictic water bodies spread along the Central Plains of Argentina. Under the premise that shallow lakes are sentinels of global climate and eutrophication, a 3-year research in ten lakes located across a climatic gradient explored which factors drove the dynamics of cyanobacterial assemblages frequently driving to bloom prevalence. Contrarily to what is expected, the effect of seasonal temperature on cyanobacteria was subordinated to both the light environment of the water column, which was on turn highly affected by water level conditions, and to nutrient concentrations. Monthly samplings evidenced that cyanobacterial assemblages presented a broad-scale temporal dynamics mostly reflecting inter-annual growth patterns driven by water level fluctuations. Both species composition and biovolume gradually changed across a gradient of resources and conditions and hence, the scenario in each individual lake was unique with patterns at different temporal and spatial scales. More than 35 filamentous and colonial morphospecies constituted the assemblages of Pampean lakes: nostocaleans and chroococcaleans were inversely correlated in the prevailing interannual 3-cycled patterns. [Display omitted] • Bloom forming cyanobacteria prevail in shallow lakes immersed in impacted landscapes. • Interannual water level changes affect light conditions hence driving bloom dynamics. • Phosphorus and light interplay influence cyanobacterial assemblage structure. • Cyanobacterial blooms persist all year round in many pampean lakes. • Species temporal replacement evidences changes of morphological traits. Light conditions associated to water level fluctuations cause cyanobacterial bloom prevalence in eutrophic Pampean shallow lakes. [ABSTRACT FROM AUTHOR]