Historical records of the Nile water level provide a unique opportunity to investigate the possibility that solar variability influences the Earth's climate. Particularly important are the annual records of the water level, which are uninterrupted for the years 622–1470 A.D. These records are non-stationary, so that standard spectral analyses cannot adequately characterize them. Here the Empirical Mode Decomposition technique, which is designed to deal with non-stationary, nonlinear time series, becomes useful. It allows the identification of two characteristic time scales in the water level data that can be linked to solar variability: the 88 year period and a time scale of about 200 years. These time scales are also present in the concurrent aurora data. Auroras are driven by coronal mass ejections and the rate of auroras is an excellent proxy for solar variabiliy. Analysis of auroral data contemporaneous with the Nile data shows peaks at 88 years and about 200 years. This suggests a physical link between solar variability and the low-frequency variations of the Nile water level. The link involves the influence of solar variability on the North Annual Mode of atmospheric variability and its North Atlantic and Indian Oceans patterns that affect rainfall over Eastren Equatorial Africa where the Nile originates.