This study aimed to strengthen the knowledge of Didymosphenia geminata distribution in Spain, and to determine which environmental variables were related to its regional distribution and temporal changes in growth and production in two Ebro River tributary basins (Iregua and Najerilla¸ La Rioja Region). Living cells of D. geminata were present in 40% of the studied sites of both basins but only four of the sites developed massive growths. The diatom is widely distributed only in mountain areas of both basins (above 690 masl), which have low average annual air temperature (8.27 ± 0.28 ºC) and low water Soluble Reactive Phosphorus (SRP) concentration (average value 0.024 ± 0.007 ppm). Massive growths occur in sites with high light intensity, hydrological regulation of river flow and the lowest measured SRP concentrations (below 0.018 ppm SRP). We carried out an intensive spatio-temporal survey in the Lumbreras River (Iregua basin), where the first massive growth was detected in La Rioja Region. The highest cell densities (1.6 × 105 cells cm−2) and biomass values (480 gDWm−2) were recorded in late summer. An increase in solar radiation and slight rise in water temperature were associated with an increase in biomass over time, but always in waters with low SRP concentration, the key factor that enhances massive growth development. The alteration of the natural streamflow in the Lumbreras River by the Pajares Reservoir and the fact that water is discharged from the hypolimnion (which decreases the summer river water temperature) are important factors in understanding why D. geminata shows such an increase in biomass in a Mediterranean river. This paper provides new insights into the importance of different factors controlling D. geminata massive proliferations in the Mediterranean climate zone, where it is assumed that the species should not develop such massive growths, compared to temperate zones where the majority of previous studies have been carried out. We suggest that changing the reservoir management strategy would be a very important contribution to the control of such significant developments.