Short-term changes in shallow bathymetry affect the coastal zone and therefore their monitoring is an essential task in coastal planning projects. This study provides a novel approach for monitoring shallow bathymetry change based on drone multispectral imagery. Particularly we apply a shallow water inversion algorithm on two composite multispectral datasets being acquired five months apart in a small Mediterranean sandy embayment (Chania, Greece). Initially, we perform radiometric corrections using proprietary software and following we combine the bands from standard and multispectral cameras resulting in a six-band composite image suitable for applying the shallow water inversion algorithm. Bathymetry inversion results showed good correlation and low errors (< 0.3m) with sonar measurements collected with an uncrewed surface vehicle (USV). Bathymetry maps and true-color orthomosaics assist in identifying morphobathymetric features representing crescentic bars with rip channel systems. The temporal bathymetry and true-color data reveal important erosional and depositional patterns, which were developed under the impact of winter storms. Furthermore, bathymetric profiles show that the crescentic bar appears to migrate across and along-shore over the 5-months period. Drone-based multispectral imagery proves to be an important and cost-effective tool for shallow seafloor mapping and monitoring when it is combined with shallow water analytical models.