Prolonged droughts, worsened by climatic factors like El Niño, amplify harm to biodiversity, economies, and society, posing complex research challenges. We analyze the relationships between El Niño climatic indices and drought periods over Ecuador. Through spatial daily precipitation (1985-2015), we calculated the number of consecutive dry days (CDD) in climatic zones of Coastal, Andean and Amazonian regions of Ecuador, such as Rainy mega thermal (RM) (Coastal and Amazonian), Tropical mega thermal humid (TMh) (Coastal and Amazonian), Tropical mega thermal dry (TMd) (Coastal), Tropical mega thermal semiarid (TMsa) (Coastal), Tropical mega thermal semi-humid (TMsh) (Coastal), Equatorial mesothermal semi-humid (EMsh) (Andean) and Equatorial mesothermal dry (EMd) (Andean), High Mountain equatorial (HMe) (Andean). Wavelet coherence was applied between ONI, SOI, Niño 1+2, and CDD indices, obtaining significant correlations greater than 0.8 in several zones. The results showed that ONI-CDD maintained a positive correlation in RM-Amazonian, TMh (Coastal and Amazonian), EMd, and HMe. In contrast, TMsa presented negative correlations. Both correlations showed the highest values during 1995-2001. SOI-CDD were positively correlated in TMsa, while the correlation was negative in RM-Amazonian, TMh (Coastal and Amazonian), EMsh, EMd, and HMe. From 1995 to 2003 presented the highest correlation. Niño1+2-CDD showed significant positive correlations during 1995-2001 in the areas close to the Amazonian region: RM-Amazonian, TMh-Amazonian, EMd, and HMe, while the correlations were negative near the Coastal region: RM-Coastal, TMd, TMsa, TMh-Coastal and EMsh. Therefore, El Niño indices have a significant relationship with dry periods in the Amazonian and the Andean regions. In contrast, these indices have relationships with wet periods in the Coastal region. These results could be a benchmark for developing advanced studies for climate hazards