Chlorophyll-a (Chla) concentrations and ‘water-leaving’ reflectance were assessed along transects in Keweenaw Bay (Lake Superior) and in Green Bay (Lake Michigan) (two of the Laurentian Great Lakes, USA), featuring oligotrophic (0.4–0.8 mg Chla m− 3) and eutrophic to hyper-eutrophic waters (11–131 mg Chla m− 3), respectively. A red-to-NIR band Chla retrieval algorithm proved to be applicable to Green Bay, but gave mostly negative values for Keweenaw Bay. An alternative algorithm could be based on Chla fluorescence, which in Keweenaw Bay was indicated by enhanced reflectance near 680 nm. Bands 7, 8 and 9 of the Medium Resolution Imaging Spectrometer (MERIS) have been specifically designed to detect phytoplankton fluorescence in coastal waters. A quite strong linear relationship was found between Chla concentration and fluorescence line height (FLH) computed with these MERIS bands. The same relationship held for observations on oligotrophic waters elsewhere, but not for Green Bay, where the FLH diminished to become negative as Chla increased. The remote sensing application of the algorithms could be tested because a MERIS scene was acquired coinciding with the day of the field observations in Keweenaw Bay and one day after those in Green Bay. For Green Bay the pixel values from the red-to-NIR band algorithm compared well to the steep Chla gradient in situ. This result is very positive from the perspective of satellite use in monitoring eutrophic inland and coastal waters in many parts of the world. Implementation of the FLH relationship in the scene of Keweenaw Bay produced highly variable pixel values. The FLH in oligotrophic inland waters like Lake Superior appears to be very close to or below the MERIS detection limit. An empirical algorithm incorporating three MERIS bands in the blue-to-green spectral region might be used as an alternative, but its applicability to other regions and seasons remains to be verified. Moreover, none of the algorithms will be suitable for mesotrophic water bodies. The results indicate that Chla mapping in oligotrophic and mesotrophic areas of the Great Lakes remains problematic for the current generation of satellite sensors.