AbstractThe river Elbe is a large eutrophic lowland river with high primary production and high phytoplankton biomass in the growing season. The objective of the study was to gain basic knowledge of the role of dead zones for phytoplankton distribution and the oxygen balance of the river Elbe. At two sampling stations water temperature, oxygen concentration, conductivity, pH value, turbidity, and chlorophyll fluorescence were measured with high precision to learn about the distribution of these parameters across the cross‐sections. The structures indicate differences in the intensity of physical and biological processes between the shallow waters near the shores, which are characterized by groyne fields, and the deep bulk flow. The conductivity clearly shows the high transverse mixing intensity in the groyne fields in contrast to the bulk flow. Groyne fields and the first, the groyne head near margin lamella of the bulk flow can be regarded as a unit. Groyne field results indicate higher primary production of phytoplankton, oxygen release, and higher pH. The turbidity of water entering the groyne fields decreases rapidly because of sedimentation within a short time. The groyne head lamella of the bulk flow sometimes shows higher chlorophyll fluorescence than the central lamella of the bulk flow and the water of the groyne field. The processes which contribute to the observed distribution are discussed, but could not yet be quantified. A modification of the dead zone model is proposed.