First we present a definition of an oceanographic observatory, and then through two concrete case studies we present operative autonomous tools for support observatories in two different environments: the coastal lagoon using fixed stations, and in the open sea using drifting instrumented buoys system as pelagic observatory. The perspective of data collection of basic information useful to develop bio-indicator and to establish times series is highlighted for ecological and monitoring studies in an ecosystemic approach. Finally on the basis of those experiences we first present a proposal of new research project ‘Seaobserver’ linked to ‘Seaorbiter’ a futuristic large drifting platform dedicated to open sea monitoring, and then ‘IJAFE’ a web resource centre for applied acoustics in fisheries and ecosystems.