Clay induced turbidity is the major cause of complex changes in the ecosystem of coastal water areas. The accuracy of the algorithms for the assessment of the clay concentration may suffer significantly from the presence of other substances like Algal chlorophyll or dissolved organic matter, highly influencing the optical properties of the water. The objective of this study was to develop an accurate and robust algorithm for the clay concentration retrieval using high spectral resolution hyperspectral data. In order to provide necessary information for the spectral analysis of the water samples, a controlled experiment was arranged. Carefully weighted clay portions were diluted in water and reflectance spectra were recorded using a field spectrometer. Traditionally simple algorithms are used to estimate the remotely sensed water quality variables. In this paper a novel algorithm based on the principle of spectral angle measure is presented. The accuracy of the proposed algorithm was just slightly better compared to the band-ratio algorithm, but it is more robust against the effects of other optically detectable substances and noise.