Bed level, bed surface grain size, and water discharge measurements along the Bovenrijn, Waal, Pannerden Channel, IJssel, and Nederrijn were carried out by Rijkswaterstaat. The .xlsx file 'Data_Bed level_D50_D90_Discharge_Bovenrijn_Waal_Pannerden_Nederrijn_IJssel' contains 12 tabs: 1. Bed elevation of the river Waal 2019-2020 (m+NAP): multibeam data, covering river km 857.5-953.9 (main channel only), with data points every 100 m. Data are cross-section averaged. 2. Bed elevation of the river Pannerden Canal-Nederrijn 1928-2002 (m+NAP): single-beam data, covering river km 868-970 (main channel only), with data points every 1 km. Data are cross-section averaged. 3. Bed elevation of the river Pannerden Canal-Nederrijn 2002-2020 (m+NAP): multibeam data, covering river km 867.6-970 (main channel only), with data points every 100 m. Data are cross-section averaged. 4. Bed elevation of the river IJssel 1941-2002 (m+NAP): single-beam data, covering river km 879-1005 (main channel only), with data points every 1 km. Data are cross-section averaged. 5. Bed elevation of the river IJssel 2002-2020 (m+NAP): multibeam data, covering river km 878.7-1005.9 (main channel only), with data points every 100 m. Data are cross-section averaged. 6. D50 of the river Pannerden Canal-Nederrijn 1966-2020 (mm): bed surface grain size (characteristic diameter D50), covering river km 868-989, with data points every 500 m. 7. D90 of the river Pannerden Canal-Nederrijn 1966-2020 (mm): bed surface grain size (characteristic diameter D90), covering river km 868-989, with data points every 500 m. 8. D50 of the river IJssel 1966-2020 (mm): bed surface grain size (characteristic diameter D50), covering river km 879-1006, with data points every 500 m. 9. D90 of the river IJssel 1966-2020 (mm): bed surface grain size (characteristic diameter D90), covering river km 879-1006, with data points every 500 m. 10. D90 of the river Bovenrijn-Waal 1966-2020 (mm): bed surface grain size (characteristic diameter D90), covering river km 849-952, with data points every 500 m. 11. Water discharge data at the Bovenrijn and Waal rivers 1971-2020 (m3/s). 12. Water discharge data at the Bovenrijn and IJssel rivers 1956-2020 (m3/s). The bed level data was corrected for the single beam to multi beam transition using the method suggested by Ylla Arbos et al. (2021).