Data on phytoplankton in the Elbe River near Hamburg from 2006 to 2023. This dataset comprises the results of a monthly survey of phytoplankton at two sites along the Elbe River in Hamburg (Zollenspieker and Seemannshöft). Data was collected as part of the Water Framework Directive. The phytoplankton contained in the routinely collected water samples was concentrated in sedimentation chambers (Uthermöhl). Finally, reverse microscopy was used to examine the phytoplankton taxa, cell number and biovolume.