In winter 2008-2009, Lake Occhito, a strategic multiple-uses reservoir in South Italy, was affected by an extraordinary Planktothrix rubescens bloom. P. rubescens is a filamentous potentially toxic cyanobacterium which has recently colonized many environments in Europe. A number of studies is currently available on the use of remote sensing techniques to monitor different fresh water cyanobacteria species. By contrast no specific applications are available on the remote sensing monitoring of P. rubescens. In this paper we present a specific algorithm, based on Water Leaving Reflectances (WLR) from MERIS data, atmospherically corrected using the Aerosol Optical Thickness (AOT) retrieved by MODIS data, to detect P. rubescens blooms. The high accuracy in AOT data, provided by MOD09 surface reflectance product, at 1km spatial resolution, allowed obtaining a good correlation between the WLR and the P. rubescens chlorophyll-a concentrations measured in the field, through multiple stations fluorometric profiles. A modified Normalized Difference Chlorophyll index (NDCI) algorithm is presented. The performance of the proposed algorithm has been successfully compared with other specific algorithms for turbid productive waters. We demonstrated how important is to verify the spectral behaviour of bio-optical parameters in order to develop an ad hoc algorithm that better performs with respect to standard algorithms.