Estuaries are among the earth's most valuable and productive environmental resources. To further our understanding of the impact of human activities on estuaries, there is a need for appropriate statistical methods for analyzing estuarine data. Estuaries possess a number of features that must be considered during spatial data analyses. Estuaries are irregularly shaped non-convex regions. Therefore, Euclidean distance may not be an appropriate distance metric for spatial analyses of estuaries, especially if the line segment connecting two sites intercepts land. Furthermore, some environmental variables may take deterministic values at estuarine boundaries. For example, shorelines are saturated with dissolved oxygen, and the salinity at estuarine mouths should be close to that of the ocean. This paper considers methods for spatial modelling and prediction using different distance metrics, and under fixed boundary conditions. These methods are illustrated using data from Charleston Harbor, an estuary on the coast of South Carolina, USA © 1998 John Wiley & Sons, Ltd.