Within the framework of Perseus and AegeanMarTech projects, multidisciplinary bio-optics experiments were conducted in the optically complex, permanently stratified waters of the NE Aegean Sea. We were able to obtain the particle size distribution (PSD) slope, using different optical sensors: (a) WET Labs ECO-B3B backscattering sensor measuring VSF at three wavelengths (470, 532, and 650 nm); (b) WET Labs C-Star transmissometer (660 nm) and Chelsea ALPHAtracka MKII (470 nm); and (c) Laser In Situ Scattering and Transmissometry – LISST-Deep. Values of the PSD slope estimated by all three methods were found to be within the ranges predicted by Mie theory and the literature. The optical backscattering ratio, bbp, was calculated from bbp(660) and cp(660) and subsequently the bulk index of refraction (np) was estimated as a function of the backscattering ratio and the PSD slope. In July 2014, the values of np varied between ~1.01 and >1.24 (mean 1.12±0.08), which fall between phytoplankton- and mineral-dominated waters. According to the spatial distribution of np two water layers could be identified, associated with different particle composition: (a) Black Sea water (BSW) and Levantine waters (LW) (from the surface to ~65 m depth) that appear to be dominated by material with mean index of refraction 1.13; and (b) the near-bottom layer which exhibited high np, >1.24, the latter attributed to mineral particles with high bulk index of refraction resuspended from the sea floor.