A study was undertaken to quantify dune migration in Portsmouth Harbor, New Hampshire, USA from repeat high-resolution multibeam echosounder (MBES) surveys. Repeat MBES surveys were conducted in June 2007 and July 2008 over periods ranging from 6 hours to 7 days in order to capture the response of dune morphology to ebb-flood and spring-neap tidal cycles. A new technique was developed for detecting bedform migration. This approach utilizes a fingerprint-detection algorithm (Bishnu et al., 2002) to convert the bathymetric surface to a binary map of bedform crests, which are subsequently tracked using a spatial cross-correlation technique (Duffy and Hughes-Clarke, 2005). Acoustic current-meter observations from July 2008 provided context for the observed bedform-migration patterns, and were subsequently used to compute bed shear stress. Results indicate that dune migration occurred over periods as short as 6 hours. Dune migration distances in excess of 2 m were observed over 6- and 7-day periods.