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Hydrological droughts are events of prolonged water scarcity and cause many devastating impacts. It is, therefore, extremely crucial to understand their spatiotemporal evolution to guide prevention and mitigation policies. The Gravity Recovery and Climate Experiment (GRACE, April 2002–June 2017) and GRACE Follow‐On (GRACE‐FO, June 2018 until the present) missions have been used to study large‐scale droughts of almost two decades. But characterizing droughts during the between missions gap period of 2017 and 2018 has not been well addressed and will be covered here. To bridge the gap, an innovative Bayesian convolutional neural network is developed to reconstruct the missing signals from hydroclimatic inputs. The reconstruction fields and existing signals are then used to explore regions that have experienced consecutive water storage deficits during the 2017–2018 gap. We found many regions of the northern midlatitudes exhibiting moderate to exceptional droughts in terms of water storage deficits, among which parts of Pakistan and Afghanistan, and Iberian Peninsula experienced exceptional droughts lasting for more than 1 year with the maximum deficits (−4.4 ± 0.8 and −7.2 ± 1.1 cm, respectively) being over 50% of the seasonal storage variations. Comparisons with climate indicators show that the identified droughts are predominantly caused by continuous below‐normal precipitation. The recovery process correlates generally well with the accumulation rate of precipitation surpluses (the correlation coefficient (R) can be up to 0.92). Besides, the reconstructed signals, which have R > 0.7 with the testing GRACE(‐FO) data in over 90% of the globe, reliably maintain the data continuity and therefore they are recommended for hydro‐climatological studies. Key Points: The missing terrestrial water storage anomaly signals between the 2017–2018 Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow‐On gap are reconstructed by Bayesian deep learningHydrological droughts overlapping with this gap period are characterized and quantifiedThe northern midlatitudes experienced continuous water storage deficits as a result of precipitation deficiency [ABSTRACT FROM AUTHOR]