A dataset of 224 Medium Resolution Imaging Spectrometer (MERIS) full resolution satellite images were processed to retrieve the concentration of coloured dissolved organic matter (CDOM) in a hypertrophic estuary (Curonian Lagoon, Lithuania and Russia). Images covered a period of 7 months, spanning from the ice melting (March) to the late summer (September) of 7 consecutive years (2005-2011). The aim of the study was to analyse the spatial and temporal variations of CDOM, by focusing on the main regulating factors (riverine discharge, sea-lagoon water exchange, water temperature, chlorophyll a, wind) in a large estuary. The working hypothesis is that CDOM distribution may reveal distinct, site specific seasonal patterns. Our results demonstrated that CDOM concentrations at the whole lagoon level were elevated (1.5-4 m-1) and slightly but significantly higher in spring (1.50 m-1 on average) compared to the summer (1.45 m-1 on average). This is due to very different flow of CDOM-rich freshwater from the main lagoon tributary in spring compared to summer. They also highlight macroscopic differences among areas within the lagoon, depending on season, suggesting a complex regulation of CDOM in this system. Significant factors explaining observed differences are the dilution of lagoon water with CDOM-poor brackish water, regeneration of large amounts of dissolved organic matter from sediments and combinations of uptake/release from phytoplankton. CDOM and its variations are understudied due to inherent methodological and analytical difficulties. However, this pool has a demonstrated relevant role in the biogeochemistry of aquatic environments. We speculate that the dissolved organic pool in the Curonian Lagoon has a mainly allochthonous origin in the high discharge period and an autochthonous origin in the summer, algal bloom period. Both positive and negative relationships between CDOM and phytoplankton suggest that pelagic microalgae may act as a source or as a sink of this pool, in particular when inorganic nutrients are limiting.