Unusual difficulties are encountered when characterizing the spatial distribution of the properties that collectively define the state of estuaries. Due to the variability of these estuarine conditions, greater sampling efforts are often necessary to describe estuarine environments, as compared to other aquatic systems. That is why in coastal management studies, where the collection of data is sometimes very difficult and time-consuming, a robust sampling strategy is essential. The aim of this study is to design a spatial sampling strategy for estuarine sediments, using prior information on the spatial variation of sediment granulometry. Systematic unaligned sampling with a grid cell size of 750×500 m was chosen on the basis of semi-variogram analysis, and was shown to have distinct advantages. This design was sampled for sediment parameters using a GPS-receiver and mapped within the digitized shoreline of the estuary. The estuary shoreline was digitized on the basis of aerial ortho-photography with tidal ebb determination. The sampling is intended to define the boundaries of environmental management areas for the Sado Estuary, situated on the west coast of Portugal. The research represents one of the initial phases in the development of a Sado Estuary environmental management system integrated into a Geographic Information System.