Followingthe Four Rivers Project, cyanobacterial blooms have been frequently observed in the upstream of the installed weirs. The aim of this study was to characterize the major environmental factors that are associated with the cyanobacteria dominance in Baekje Weir (Geum River) and Juksan Weir (Youngsan River) based on intensive experiments and systematic data mining methods. The factors related to the cyanobacteria dominance include7-days cumulative rainfall (APRCP7), 7-days averaged flow (Q7day), water temperature (Temp), stratification strength (${\Delta}T$), electronic conductivity (EC), DO, pH, $NO_3-N$, $NH_3-N$, TN, TP, $PO_4-P$, Chl-a, Fe, BOD, COD, TOC, and $SiO_2$. The most highly correlatedfactors to the dominant cyanobacteria were found to be EC, Temp, Q7day, $PO_4-P$ in theBaekje Weir. On the other hand, those dominant in the Juksan Weir were ${\Delta}T$, TOC, Temp, EC and TN. The EC showed a strong correlation with cyanobacteria dominance in both weirs because a high EC represents a persisted low flow condition. The cyanobacteria dominance was as high as 56 % when the EC was equal or greater than $418{\mu}S/cm$ in Baekje Weir. It was as high as 63% when the ${\Delta}T{\geq}2.1^{\circ}C$ in the Juksan Weir. However, nutrients showed a minor correlation with cyanobacteria dominance in both weirs. The results suggest that the cyanobacteria dominate in astate where the water flow rate is low, water temperature is high and thermal stratification is strengthened. Therefore, the improvement of flow regimes is the most important to prevent persistent thermal stratification and formation of cyanobacteria bloom in theBaekje and JuksanWeirs.