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Droughts are projected to increase in intensity and frequency with the rise of global mean temperatures. However, not all drought indices equally capture the variety of influences that each hydrologic component has on the duration and magnitude of a period of water deficit. While such indices often agree with one another due to precipitation being the major input, heterogeneous responses caused by groundwater recharge, soil moisture memory, and vegetation dynamics may lead to a decoupling of identifiable drought conditions. As a semi-arid basin, the Limpopo River Basin (LRB) is a severely water-stressed region associated with unique climate patterns that regularly affect hydrological extremes. In this study, we find that vegetation indices show no significant long-term trends (S-statistic 9; p-value 0.779), opposing that of the modeled groundwater anomalies (S-statistic -57; p-value 0.05) in the growing season for a period of 18 years (2004–2022). Although the Mann-Kendall time series statistics for NDVI and drought indices are non-significant when basin-averaged, spatial heterogeneity further reveals that such a decoupling trend between vegetation and groundwater anomalies is indeed significant (p-value < 0.05) in colluvial, low-land aquifers to the southeast, while they remain more coupled in the central-west LRB, where more bedrock aquifers dominate. The conclusions of this study highlight the importance of ecological conditions with respect to water availability and suggest that water management must be informed by local vegetation species, especially in the face of depleting groundwater resources.