River bathymetry surveys were collected in the summer and fall of 2016 along the lower Chetco River, Oregon. These surveys were collected using a real time kinematic global positioning system (RTK-GPS) and an echo sounder mounted on a motorboat and also behind a kayak at various cross sections and longitudinal profiles along the river. These datasets were collected in support of a funded effort investigating the cause of salt water intrusion that has taken place at the water intake facility for Harbor City, Oregon. The surveys were collected at sections approximately 0.4 river miles downstream to 0.8 river miles upstream of the Harbor City water intake structure and also at the city of Brookings water intake facility, located approximately 1.6 river miles upstream of the Harbor City intake structure.