NavCleaner is a program to filter, smooth and interpolate underwater navigation data (USBL, DVL, hybrid). NavCleaner is optimised to process the navigation data of the MARUM ROV QUEST4000 but it can be used to process dive track data from other instruments as well. All calculations are done internally on projected coordinates using the most relevant WGS84 UTM/UPS zone in order to minimize errors. As inputs, NavCleaner can read USBL, DVL, depth, altitude (height above bottom), heading, pitch, and roll data timeseries. A configuration file enables NavCleaner to read a variety of text file formats. The program outputs comma-separated files containing the filtered, smoothed and 1 Hz interpolated navigation timeseries (both geographic coordinates and UTM/UPS coordinates) for all input data timeseries. If both USBL and DVL data are used as inputs, NavCleaner also merges the USBL and DVL data to create a hybrid navigation track. Optionally, NavCleaner can compute the coordinates for every observations in the dive report (Excel format).