AbstractThe development and validation of an atmospheric correction algorithm designed for the Medium Resolution Imaging Spectrometer (MERIS) with special emphasis on case‐2 waters is described. The algorithm is based on inverse modelling of radiative transfer (RT) calculations using artificial neural network (ANN) techniques. The presented correction scheme is implemented as a direct inversion of spectral top‐of‐atmosphere (TOA) radiances into spectral remote sensing reflectances at the bottom‐of‐atmosphere (BOA), with additional output of the aerosol optical thickness (AOT) at four wavelengths for validation purposes. The inversion algorithm was applied to 13 MERIS Level1b data tracks of 2002–2003, covering the optically complex waters of the North and Baltic Sea region. A validation of the retrieved AOTs was performed with coincident in situ automatic sun–sky scanning radiometer measurements of the Aerosol Robotic Network (AERONET) from Helgoland Island located in the German Bight. The accuracy of the derived reflectances was validated with concurrent ship‐borne reflectance measurements of the SIMBADA hand‐held field radiometer. Compared to the MERIS Level2 standard reflectance product generated by the processor versions 3.55, 4.06 and 6.3, the results of the proposed algorithm show a significant improvement in accuracy, especially in the blue part of the spectrum, where the MERIS Level2 reflectances result in errors up to 122% compared to only 19% with the proposed algorithm. The overall mean errors within the spectral range of 412.5–708.75 nm are calculated to be 46.2% and 18.9% for the MERIS Level2 product and the presented algorithm, respectively.