Bio-optical measurements were carried out on eutrophic Lake Zug and oligotrophic Lake Lucerne, to provide data and models for the in situ calibration of multispectral imagery collected in 1991, during an AVIRIS flight over Central Switzerland. The results indicate that Secchi depth, chlorophyll and total suspended solid concentrations, vertical extinction coefficient, absorption coefficient and irradiance reflectance in the PAR region can be used to discriminate between the two lakes. Dissolved organics concentration, scattering and total attenuation coefficients estimates, as well as backscattering probability, are less acceptable, because of instrumental limitations. Relationships between optical and water quality parameters were investigated and found to behave according to accepted theoretical frameworks. Both lakes exhibited vertical and horizontal heterogeneities in chlorophyll and turbidity, and had contrasting mean bio-optical characteristics: although suspended solid concentrations were similar, transparency was lower in Lake Zug, but reflectance was substantially higher in Lake Lucerne. Water colour determined by chromaticity analysis was blue-green in Lake Lucerne and green in Lake Zug. Reflectance spectra simulated through a three-component optochemical model did not completely match those derived from in situ measurements, because of lack of site-specific optical cross-sections for suspended minerals and dissolved organics. The monitoring of water quality in subalpine lakes by remote sensing, both with present and future technology, is discussed and considered as possible, provided that their optical behaviour is known, and preferably expressed by a valid optochemical model.