We compared the longitudinal plankton development in the two large rivers Rhine and Elbe by means of four Lagrangian sampling campaigns performed within the time span 2009–2011. The campaigns revealed low chlorophyll concentrations in the Rhine along a long river stretch (Rhine‐km 170 to 854) with maximum values below 5 µg L−1 in 2010. In contrast, the Elbe (Elbe‐km 4 to 582) showed high and longitudinally increasing chlorophyll concentrations with maximal values of 174 µg L−1 in 2009 and 123 µg L−1 in 2011. Additional samples of the benthic bivalves along the river stretches revealed high densities of the filter feeders in the Rhine that could potentially explain losses of plankton production. Their densities in the Elbe were significantly lower, making important losses to benthic filter feeders unlikely. However, strong phytoplankton growth was observed during the sampling campaign in 2011 in the Rhine coinciding with a low discharge event. This resulted in an exceptionally high chlorophyll value of up to 244 µg L−1 in the lower river sections, a value that was not reached in the last two decades of continuous water quality monitoring in the Rhine. Even though we cannot fully explain this phenomenon, it shows that phytoplankton has a high growth potential in the Rhine but is usually controlled by other mechanisms. Tributaries represented an additional and important source of plankton biomass and suspended substances in the Rhine, whereas they primarily diluted the plankton concentrations in the Elbe. Copyright © 2015 John Wiley & Sons, Ltd.