Changes in longitudinal distribution of eutrophication parameters in brackish and marine layers of a stratified karstic estuary have been investigated from December 1988 until October 1989 on a gradient between a pristine and a moderately polluted area. In the estuary, only marine phytoplankton blooms were found to develop. Near the head of the estuary, blooms develop below the halocline. Marine phytoplankton is fed by nutrients released from the decay of sinking freshwater phytoplankton. Phytoplankton growth is P-limited. Hypoxia near the bottom follows the decay of occasionally large quantities of allochtonous freshwater and of autochthonous marine phytoplankton. In the lower estuary, blooms have been observed to develop in the brackish layer above the halocline due to high salinity in the layer and the existence of a local anthropogenic nutrient input