This project measured spectral reflectance for variety of submerged aquatic vegetation (SAV) species and bare substrate types found in Estonia and Swedish coastal waters in the Baltic Sea. The dataset was collected between 2011-2012 during various field campaigns. Target samples were measured within the 350 to 900 nm wavelength range under sun light conditions using Ramses (TriOS GmbH, Germany) measurement set, which consisted of two simultaneously operated sensors: irradiance and radiance sensors. The radiance sensor measured upwelling spectral radiance Lu (W m-2 nm-1 sr-1) and irradiance sensor measured downwelling spectral irradiance Ed (W m-2 nm-1). Remote sensing reflectance (Rrs) was calculated as the ratio of Lu/Ed (sr-1). All target samples were taken out of the water before the measurement.