Data were collected in 2015 and 2016 to provide information about spatial variations in water depth and river bed morphology (including bedform height) on the South Saskatchewan River, Canada. Water depth measurements were obtained with a Navisound NS 215 system and a Reson TC 2024 200kHz high-resolution dual frequency single beam echo sounder (SBES) operating at a sampling frequency of 10hz. Data were geolocated via a Leica 1230 Real-Time Kinematic (RTK) dGPS system. Data were collected in 2015 (between 7th and 9th September) and 2016 (between 2nd and 14th September) as part of NERC project NE/L00738X/1. Full details about this dataset can be found at https://doi.org/10.5285/14c80b71-6eb6-4dba-a298-b95a37059f55