Cell death drives the magnitude and community composition of phytoplankton and can result in the conversion of particulate organic carbon to dissolved organic carbon (DOC), thereby affecting carbon cycling in the aquatic food web. We used a membrane integrity probe (Sytox Green) to study the seasonal variation in the percentage of viable cells in the phytoplankton population in an estuary in the northern Baltic Sea for 21 months. The associated dissolved and particulate organic matter concentrations were also studied. The viable fraction of phytoplankton cells varied from \ 20% to almost 100%, with an average of 62%. Viability was highest when a single phytoplankton group (diatoms or dinoflagellates) dominated the community. Viability of sinking phytoplankton cells, including some motile species, was in general as high as in surface water. Changes in viability were not closely related to nutrient concentrations, virus-like particle abundance, seawater temperature or salinity. There was a weak but significant negative correlation between viability and DOC, although at this location, the DOC pool was mainly influenced by the inflow of riverine water. This study demonstrates that cell viability, and its relationship with carbon export, is highly variable in the complex microbial populations common within estuarine and coastal marine ecosystems.