The understanding of soil moisture dynamics is important for agricultural productivity as well as water resource management. This study investigates the spatial variations of drought in relation to soil moisture, across three different soil layer depths in Nigeria, using the established drought indices. Multiple soil moistures at different levels within the soil profile were considered to investigate their respective changes between 1981 and 2022. Pearson’s correlation coefficient (r) was used to assess the strength of complex relationship between the drought indices and historical soil moisture. Rainfall Anomaly Index (RAI) correlated best with soil moisture at 0–5 cm in 28 states, with r ranging from 0.52 to 0.86. Soil moisture in the arid areas correlated more closely with RAI but relates better with PHDI in the humid regions. This study would give invaluable insights to stakeholders for the enhancement of resilience in agricultural productivity and drought readiness in Nigeria.