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 chlorophyll‐a fluorescence from the long‐term BOUSSOLE time series, at all three time scales. 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 (~400 km) and are tightly connected with seasonal MxLD changes. Intraseasonal SChl fluctuations occur at smaller spatial scales (~100 km), 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 (~1,000 km) 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.