Abstract. Understanding how water resources vary at different temporal and spatial scales in response to climate is crucial to inform long-term management. Climate change impacts and induced trends may indeed be substantially modulated by low-frequency (multi-year) variations, whose strength varies in time and space, with large consequences on risk forecasting systems. In this study, we present a spatial classification of precipitation, temperature and discharge variability in France, based on a fuzzy clustering and wavelet spectra of 152 near natural watersheds between 1958 and 2008. We also explore phase-phase and phase-amplitude causal interactions between time scales of each homogeneous region. Three significant time scales of variability are found in precipitation, temperature and discharge: 1 year, 2–4 years and 5–8 years. The magnitude of those time scales of variability is however not constant over the different regions. For instance, Southern regions are markedly different from other regions, with much lower 5–8 years variability and much larger 2–4 years variability. Several temporal changes in precipitation, temperature and discharge variability are identified during the 1980s and 1990s. Notably, we note a sudden decrease in annual temperature variability in the mid 1990s in the Southern half of France. Investigating cross-scale interactions, our study reveals causal and bi-directional relationships between higher and lower-frequency variability, which may feature interactions within the coupled land-ocean-atmosphere systems. Interestingly, however, even though time-frequency patterns (occurrence and timing of time scales of variability) were similar between regions, cross-scale interactions are far much complex, differ between regions, and are not systematically transferred from climate variability (precipitation and temperature) to hydrological variability (discharge). Phase-amplitude interactions are indeed absent in discharge variability, although significant phase-amplitude interactions are found in precipitation and temperature. This suggests that watershed characteristics cancel the negative feedback systems found in precipitation and temperature.This study allows for a multi-time scale representation of hydro-climate variability in France, and provides unique insight into the complex non-linear dynamics of this variability, and its predictability.