Mediterranean and Baltic Seas are somehow two different worlds in term of biogeochemical dynamics, but some challenges they face are common, especially those related to toxic pollutants and harmful algal blooms that may affect ecosystem, aquaculture and tourism. Toxicity can be linked to algal blooms, which are operationally monitored by different research teams, usually by ships. Satellites may instead provide a more informative synoptic view, that can be also assimilated by the forecast modelling systems, as that one managed by OGS within the CMEMS-MED-MFC.