This study investigates meteorological drought characteristics across three climatic zones in Benin using the SPEI (Standardized Precipitation Evapotranspiration Index) and SPI (Standardized Precipitation Index). A comprehensive statistical approach was employed, including the Mann–Kendall trend test, drought duration and intensity analysis, Pearson correlation, cross-wavelet transform, and the Standardized Relative Air Humidity Index (SRHI), to assess drought patterns and trends. The findings indicate increasing consistency between SPI and SPEI trends at longer timescales, though significant regional variations persist. In Zone 1 (northern Benin), SPI exhibited an increasing trend across all timescales, whereas SPEI demonstrated a decreasing trend at shorter timescales. In contrast, in Zones 2 (central Benin) and 3 (south Benin), both indices generally displayed a decreasing trend, except at the one-month scale. An analysis of drought duration and intensity revealed that, at shorter timescales (SPI and SPEI at 1- and 3-month intervals), the longest droughts occurred in Zones 1 and 3, while the most intense events were recorded in Zone 2. At longer timescales (SPI and SPEI at 6- and 12-month intervals), Zone 2 experienced the longest droughts, whereas Zone 3 exhibited the highest intensities. These findings illustrate the need for monitoring strategies tailored to a given area’s characteristics. Despite these insights, data uncertainties and regional differences present challenges for drought investigation. Future studies should incorporate more datasets and investigate different drought indices to improve decision-making and improve strategies for safeguarding Benin’s agricultural sector, ecosystems, and food supply.