Understanding long‐term variations of ocean ecosystems requires untangling the time scales involved in their natural fluctuations. We applied a temporal decomposition procedure to two decades of satellite ocean color observations to characterize the time variability of surface Chlorophyll‐a (SChl) in the Mediterranean Sea. In order to assess the reliability of the satellite data at capturing intraseasonal, seasonal and interannual variability, we first show that satellite SChl data compare well with field data of phytoplankton fluorescence from the long‐term BOUSSOLE time series, at all three timescales. The decomposition procedure is then applied to satellite SChl and to mixing‐layer depth (MxLD) data from an ocean reanalysis, both at the scale of the entire Mediterranean Sea. Our results reveal similar amplitude for the seasonal and intraseasonal SChl variations in the Northwestern bloom region, together explaining about 90% of the SChl variance. Coherent seasonal SChl variations occur at the scale of the bloom region (~400km) and are tightly connected with seasonal MxLD changes. Intraseasonal SChl fluctuations occur at smaller spatial scales (~100km), suggesting they would be generated by storms although they weakly correlate to variations of the MxLD reanalysis. Over the oligotrophic part of the Mediterranean Sea, about 80% of the variability in both SChl and MxLD are explained by basin‐scale (~1000km) seasonal variations. Intraseasonal variability occurs at much smaller spatial scales, typical of mesoscale activity (~30 km). These results support the hypothesis that seasonal SChl variations are driven by changes in MxLD, while mesoscale activity and storms drive the intraseasonal SChl fluctuations.

Plain Language Summary

In the context of our changing climate, an ongoing challenge is to be able to reliably detect and attribute trends in ocean color records of surface chlorophyll‐a (SChl), which is the only observable variable representative of the state of marine ecosystem available at global scale. However, the magnitude of the natural variability of SChl is much stronger than that of the SChl long‐term trend. Furthermore, this natural variability occurs over a large range of unrelated time scales, making it difficult to detect and attribute a climate‐driven trend. Here we focus on the variability over temporal scales that have been overlooked because their observation requires continuous measurements, i.e. fluctuations that are shorter than seasonal ones. In the case of the Mediterranean Sea, we show that such intraseasonal variations can be as large as seasonal ones, and that they may also be less predictable because they likely ensue from processes such as storms or ocean eddies.