The aim of this study was to assess in-stream retention of suspended solids (SS) and total phosphorus (TP) at low flow condition in a large watercourse, the Tisza River. The analysis was based on a longitudinal water quality profile obtained in July 2006 during a cruise along the Hungarian section of the river (nearly 600 km). Water samples were taken manually for SS and TP every half an hour (ca. 5.5 km). Additionally, concentration of SS was calculated from on-line turbidity records taken every 6 s (ca. 10 m). Velocity field was calculated with a 1D hydrodynamic model calibrated for low flow conditions. To describe the transport, a simple first-order equation was adjusted to the SS profile after estimating the potential maximum of SS that the flow with the given velocity could transport. Specific P content of SS was related to velocity to estimate longitudinal TP profile. Retention of TP amounted to 42% along the Hungarian section of the Tisza River at a flow of 110 m3 s−1. Storage reservoirs significantly influenced the longitudinal retention pattern. Upstream of Dam II (river kilometre 404), net TP retention reached 73%, while the downstream section was a source of TP.