The aim of this study was to investigate phytoplankton abundance, composition and vertical export in the highly stratified Krka estuary, Croatia. The estuary is stratified throughout the year, and an interface between fresh- and brackish water plays an important role in production and degradation of biogenic matter. Vertical export of particulate organic carbon (POC), phytoplankton carbon (PPC) and faecal pellet carbon (FPC) was studied by deploying sediment traps in the middle and lower reach of the estuary and in the adjacent coastal zone. Zooplankton faecal pellet (FP) production experiments were conducted to provide additional information on the potential contribution of FP to the total carbon flux. High suspended concentrations of POC, chlorophyll a and phytoplankton was found in the lower reaches of the Krka estuary, adjacent to a source of anthropogenic eutrophication. The fraction of organic detritus to the total POC flux was 61–69% inside the estuary but only 7% at the marine station. This indicates that the primary producers in the surface layer of the Krka estuary are decomposed in and below the interface and then settle as detritus to the bottom. Low sedimentation rates in the coastal zone outside the estuary revealed that the eutrophication does not spread out of the estuary. Mesozooplankton played a modest role in vertical flux regulation, due to their low abundance and dominance of smaller forms as well as low faecal pellet production rates. It is concluded that processes taking place at the freshwater-seawater interface are of major importance for the vertical carbon flux in the investigated area.