Drylands are essential components of the Earth System, and dryland dynamics are strongly controlled by water availability. Long-term ground observations of hydrological parameters are often lacking in most dryland ecosystems. A series of foundational and unique water input data, including both rainfall and non-rainfall (i.e., fog and dew) components, in hyper-arid desert environments has been presented in this database. These observations provide comprehensive isotope measurements of rainfall and non-rainfall water resources, which are essential to evaluate the impacts of extreme climate events on the water cycle. The database comprised three key components: (1) a decade-long (2014−2023) event-based stable isotopes (δ²H, δ¹⁸O, and d-excess) in rainfall and non-rainfall waters at Gobabeb, (2) a two-month spatial isotope dataset (δ²H, δ¹⁸O, and d-excess) of fog collected from the central Namib Desert in 2016 and 2017, and (3) a six-decade (1963−2023) temporal dataset documenting monthly fog and rainfall amounts as well as annual Kuiseb River flooding events at Gobabeb. The detailed stable isotope data included 532 fog samples, 71 rainfall samples, 115 dew samples, and 13 groundwater samples over the past ten years (2014−2023) in the Namib Desert. Detailed descriptions of the study sites, sampling procedures, analytical methods, and data quality control are provided in this study. The uniqueness of our long-term dataset makes it an important resource for future studies investigating hydrological processes in drylands and their responses to climate change. The DOIs of the dataset can be obtained in the “Data availability” section.