The hydro-optical properties of coastal and largely off- coastal waters of the Bay of Biscay are essentially non-case 1 waters due to a wealth of factors encompassing, inter alia, extensive river discharge, wind-driven bottom sediments resuspension, development of calcifying algae, etc. This precludes the employment of standard NASA (SeaWiFS, MODIS) or ESA (MERIS) ocean colour algorithms. We developed an array of new dedicated algorithms for assessing from SeaWiFS and MODIS the abundance and areal extent of suspended minerals, endemic non-harmful algal blooms, as well as identification and mapping of areas of two harmful phytoplankton groups - Lepidodinium chlorophorum and Emiliania huxleyi. Through a thoroughly substantiated procedure of bridging of SeaWiFS and MODIS data on such optically complex waters, seasonal to decadal dynamics in the biogeochemical processes and specifically algal ecology in the Bay of Biscay is documented and related to intrinsic hydrological processes, external forcing and climatic tendencies in the area.