While the Gravity Recovery And Climate Experiment (GRACE) and its Follow-On (GFO) missions have offered valuable observations for monitoring total water storage anomalies (TWSA), their short record constrains our ability to study the complete range and long-term variability of TWSA in the Nile River Basin (NRB). Previous studies reconstructing TWSA in this region either relied on specific hydrological models or did not consider spatial correlations among the TWSA grids. Here, we employ RecNet, a deep learning model capable of providing independent TWSA observations without relying on hydrological models while considering spatial correlations, to reconstruct precipitation-driven TWSA in the NRB from 1923 to 2022. The reconstructed data are validated by comparisons with the Global Land Data Assimilation System (GLDAS), the WaterGAP Global Hydrology Model (WGHM), the water balance budget, long-term runoff data, and GRACE-REC (i.e., a global reconstruction dataset freely available online). Subsequently, the suitability of the reconstructed data for studying El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) impacts within the NRB is assessed. Dividing the NRB into four sub-regions, i.e., the Lake Victoria Basin (LVB), the Bahr el Jebel and Bahr el Ghazal basins (BJBG), Ethiopian Highlands region (EH), and the Lower Nile River Basin (LNRB), it is shown that RecNet successfully reconstructs precipitation-driven TWSA over BJBG and EH, achieving correlation coefficient (CC), normalized root mean square error (NRMSE), and Nash–Sutcliffeefficiency (NSE) of 0.94/0.11/0.88 and 0.96/0.09/0.91 during the testing period, respectively. Additionally, RecNet’s reconstruction shows better agreement with GLDAS and WGHM than GRACE-REC, correlating well with runoff and the water balance budget in these regions. The relatively poor performance in the LVB and LNRB regions could be attributed to the substantial influence of Lake Victoria and the arid climate, respectively. Correlation analysis and wavelet coherence analysis identify significant coherence between ENSO/IOD and the reconstructed TWSA in BJBG and EH, with CC values of −0.68/0.34 and −0.82/0.56, respectively. This study provides centennial reconstructed TWSA data that could be useful in climate change/variability studies and water resource management within the NRB.
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