Automated systems for observing physical, chemical and biological conditions in the sea are being implemented worldwide as part of the Global Ocean Observing System. This report describes their use in the Baltic and the Skagerrak-Kattegat areas. An evaluation of the use of FerryBox systems in the waters around Sweden shows that the quality of data from near surface waters is high, and that the frequent sampling makes possible observations of short term phenomena such as algal blooms. These events are often overlooked by infrequent sampling using research vessels, which leads to erroneous estimates of phytoplankton biomass, ecosystem carrying capacity etc. Data come from the Helsinki-Lübeck route, operated by the Finnish Institute for Marine Research and from routes in the Skagerrak-Kattegat operated by the Norwegian Institute for Water Research. FerryBox data were compared with data from traditional sampling, principally from RV Argos operated by SMHI, but also from the HELCOM databank at ICES. Observations using automated systems such as satellites, stationary platforms (buoys and piles) and FerryBox systems may contribute substantially to improving the quality of results from models describing the physical and biogeochemical conditions in Scandinavian waters. Boundary conditions for models can be obtained using measurements in the eastern North Sea and in the Skagerrak, while data assimilation from a network of buoys, FerryBoxsystems and research vessels improves the quality of model results. Today, between four and six automated oceanographic observation systems are in operation in Swedish waters, which can be compared to more than 700 for meteorological purposes. A dramatic increase in the number of observations is necessary for effective data assimilation. To make the observations useful for biogeochemical models, parameters such as inorganic nutrients, phytoplankton biomass and oxygen must be added to the basic parameters salinity and temperature. A detailed proposal for a new infrastructure for marine monitoring and operational oceanography in Sweden is put forward. FerryBox systems should be operated in collaboration with institutes in Finland, Estonia, Poland, Germany, Denmark and Norway. Coastal buoys contribute to the monitoring needs of the EU Water Framework Directive while offshore buoys are for long term climate and ecological research and for fulfilment of the EU Marine Strategy Directive . Products combining satellite data with in-situ observations should be developed. These automated systems augment monitoring using research vessels but do not replace it. SMHI, the Swedish Institute for the Marine Environment, the Swedish Water Authorities, the Swedish Environmental Protection Agency, Swedish Navy, Coast guard, Maritime Administration and Board of Fisheries are proposed to govern and operate the system, with SMHI as the lead partner. The function ‘National data host for operational oceanographic data’ is proposed, to be established at the National Oceanographic Data Centre at SMHI. A number of indicators for describing the status of the pelagic environment around Sweden are proposed. Some already exist while some are new. New ones include indicators for acidification, changes in plankton community structure and physical climate indicators. Basin wide indicators are based on measurements using a combination of sampling platforms. Other indicators are more specific, e.g. for transport between basins and inflow of water to the deep basins of the Baltic Proper.