The HYPERMAQ dataset contributes to a better description of marine optics in optically complex water bodies by providing optical and biogeochemical parameters for 180 sampling stations with turbidity and chlorophyll-a concentration ranging between 1 to 700 FNU and between 0.9 to 180 mg m-3 respectively. The HYPERMAQ dataset is composed of biogeochemical parameters (i.e. turbidity, suspended particulate matter, chlorophyll-a and other phytoplankton pigments concentrations), apparent optical properties (i.e. water reflectance from above water measurements) and inherent optical properties (i.e. absorption and attenuation coefficients) from six different study areas. These study areas include large estuaries (i.e. the Rio de la Plata in Argentina, the Yangtze Estuary in China and the Gironde Estuary in France), inland waters (i.e. the Spuikom in Belgium and Chascomus Lake in Argentina) and coastal waters (Belgium). All data were collected between April and September 2018.