Information concerning the types, patterns, and intensity of hydroclimatic variability is needed in various sectors, including water resources planning and climate change adaptation, among numerous others. In transboundary river basins, the nature of hydroclimatic variability frequently is a critical input in the treaties governing water resources allocation to competing parties and sectors. Yet, the pattern of hydroclimatic variability across Africa’s Transboundary Rivers Basins (ATRB) remains poorly investigated owing primarily to lack of access to required data. To the extent that such studies exist, they often have been conducted at different times using different data sets and reference periods, making comparisons across the continent difficult. In this paper, we make use of NASA’s Gravity Recovery and Climate Experiment (GRACE) satellite data to extend the Terrestrial Water Storage (TWS) +50 years prior GRACE era using the unique Generalized Additive Model for Location Scale and Shape (GAMLSS) approach on the Global Land Data Assimilation System Version 2 data (GLDAS V2). The results revealed a downward trend of the TWS over Africa with a decrease rate of 0.14 cm/yr. The spatial patterns of TWS in ATRB showed a significant decreasing trend for Nile, Niger, Chad, Volta, and Congo River Basins, compared to the insignificant trends for Zambezi, Okavango, Limpopo and Orange River Basins. The spatial trends in annual TWS is primarily related to the regional variation in the precipitation trends. The largest negative trend in precipitation were observed over West Africa and Sahel region. The dry trend over south Africa were intervened by wet records. The nature of these hydroclimatic patterns are explained by the significant reduction in the total precipitation and the increasing demands on water resources.