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The Ria Formosa (eastern Algarve) comprises salt and brackish marshes covering an area of almost 200 km2 with a highly unstable morphodynamic balance. Protected by a chain of barrier islands, the lagoon and its shores are located inside a nature reserve, whose territory is undergoing substantial change: encroaching urbanisation from a regional metropolis, changing use of embanked marshes (salt farming, fish farming) and cultivated marshes, and pressure from tourism. In this context, this paper sets out the first results of a research programme involving geographers from different disciplines (climatology, geomorphology, biogeography, human and economic geography). Given the specific conditions of a protected territory on the Algarve coast, it aims to highlight the value of an environmental study protocol comparing “physical” and “human” approaches to the environment and linking, on different scales, a general analysis and detailed studies of particularly unstable sectors, using appropriate mapping techniques.