This study correlated the trophic condition of two Mediterranean water bodies with different typology with their water quality characteristics. The two studied cases included Polemidia Dam, a reservoir enriched with tertiary treated wastewater in Cyprus and Lake Karla, a re-established reservoir in Greece. The aim was to identify the key environmental variables driving cyanobacteria blooming and their cyanotoxicity and therefore to address effective management tools for each one case. Annual data provided by the national water bodies authorities as well as by regular monitoring were collected and analyzed for both cases. To examine which environmental variables contribute the most to the trophic condition of the reservoirs, a PCA analysis (Principal Component Analysis) was applied because itcan assess the effect of multiple variables at the same time. In addition, through multiple linear regression analysis, we were able to correlate characteristics of the blooms with nutrients (N, P) and water temperature. As expected, temperature is not a limiting factor for bloom formation for both waterbodies. Among the variables tested, phosphorus (P) was found to be the key element for the growth of cyano-HABs in Lake Karla, while a significant reduction in the TP concentration of the recycled water used to enrich Polemidia reservoir following year 2010 altered the trends of cyano-HABs formation and their characteristics. It is anticipated that the outcomes of this study will assist in identifying the most challenging issues related to cyano-HABs in warm reservoirs in the near future conditions.