Highlights • Climate forcing explains 80% of the piezometric level variability in Portugal. • NAO is the leading pattern (40–60% of explained variability) with 6–10 year cycles. • Higher frequency fluctuations (2.5, 3.3 and 4.2 year periods) are linked to EA and SCAND. • EA is more influent in the north and SCAND in the south of the country. • Coupled NAO and EA phases are associated with extreme piezometric levels. Abstract Under the increasing risk of water scarcity, aquifer management strategies can take advantage of a deeper knowledge about the natural long-term fluctuations driven by climate patterns. This study examines the links between major large-scale atmospheric circulation modes and inter-annual to decadal oscillations in groundwater levels in Portugal. Precipitation and piezometric records (1987–2016) from two aquifer systems, Leirosa-Monte Real in the north and Querença-Silves in the south, are analyzed using wavelet transform methods and singular spectral analysis. Wavelet coherences computed between hydrologic time series and the North Atlantic Oscillation (NAO), East Atlantic (EA) and Scandinavia (SCAND) climate patterns show non-stationary relationships that are nonetheless consistent in distinct period bands. The strongest covariability occurs in the 6–10 years band for NAO, in the 2–4 years band for EA (especially after 1999) and in the 4–6 years band for SCAND (mainly after 2005). NAO is the mode playing the most relevant role with a stronger influence in the south (60% on average) than in the north (40% on average). The relatively higher frequency (<5 year period) contributions of EA and SCAND are difficult to set apart but their joint impact accounts for approximately 20% and 40% of the total variance of groundwater levels in the south and north of the country, respectively. Wavelet coherence patterns also expose transitive couplings between NAO, EA and SCAND. Often, coupled phases between climate modes mark abrupt transitions in synchronization patterns and shifts in the time-frequency domain. Extremes in groundwater storage coincide with anti-phase NAO and EA combinations: maximum piezometric levels occur during NAO-EA+ (coincidentally also SCAND+) phases while minimum levels occur during NAO+EA− phases. [ABSTRACT FROM AUTHOR]