Dissolved organic carbon (DOC) is an important fraction of organic carbon (OC) that together with colored dissolved organic matter (CDOM) plays a key role in the carbon cycling of lakes. Lake Võrtsjärv is a large and shallow eutrophic lake where water quality measurements have been carried out for a long time. The monthly characteristics of DOC and CDOM in Võrtsjärv and its input/output rivers were traced in 5-years observations. We attempted to link the hydro-morphological indices as lake area (A), water level (WL) and volume variations (Qc) with lake DOC fluxes and CDOM-DOC relationships to improve understanding of carbon fluxes in a very shallow, large and highly eutrophic lake, as well as of the possibility to estimate DOC fluxes by CDOM via remote sensing. The research questions were: how the properties and quantity of DOC, its fluxes and CDOM-DOC relationship in a very shallow, large and highly eutrophic lake are responding to 1) variable proportions of allochthonous and autochthonous processes and 2) changing hydrological conditions. The increased lake volume variation in spring caused the higher level of CDOM, signifying the terrestrial (allochthonous) DOC (DOC_Alloch) domination in Lake Võrtsjärv. The proportion of DOC_Alloch increased together with increasing WL, A and CDOM concentration. Although the generally high proportion of DOC_Alloch in Võrtsjärv, the autochthonous DOC determines the water color (CDOM/DOC) in this highly productive ecosystem with short residence time (280–365 days). Our study on DOC flux revealed that the internal carbon sources, driven by hydrological factors, contribute significantly to the role of large and shallow lakes in global carbon cycling. The further development of water color remote sensing could provide novel directions for understanding the feedbacks of lake DOC flux and changing hydrology.