The land–sea interface, or Coastal Transition Zone (CTZ), is the area that links terrestrial and marine habitats. We use here the definition of [Schaefer, 1972]: “the sea and the land adjacent to the interface, encompassing that region where terrestrial activities importantly impinge on the marine environment, marine resources and marine activities, and where marine activities importantly impinge on the environment, resources, and activities of the land”. The precise spatial scale and extent of the interface in this definition is (appropriately, we feel) ambiguous, as it depends on both the attributes of the interface at any given location, as well as the processes or features being examined. Like many ecotones, the CTZ is an area of intense interactions and enhanced productivity and biodiversity ([Levin et al., 2001]). The coastal zone is also a “keystone” habitat, providing human and ecosystem services out of proportion to its areal extent (e.g., [Costanza et al., 1997]). The coastal zone represents only 8% of the earth, but provides 20% of the oceanic production ( [Liu et al., 2000. K.K. Liu, K. Iseki and S.Y. Chao, Continental margin carbon fluxes. In: R.B. Hanson, H.W. Ducklow and J.G. Field, Editors, The Changing Ocean Carbon Cycle, Cambridge (2000), pp. 187–239.Liu et al., 2000]). Further, 60% of humans, 3.8 billion people, live within 100 kilometers of the sea ( [Vitousek et al., 1997]). This region is a nexus for transportation, production of energy, and food resources for humans. The importance of this region, both to humans and to terrestrial and aquatic ecosystems, makes it crucial that we understand the processes and interactions in this habitat. The coastal transition zone, however, presents a number of difficult research challenges. While these challenges are qualitatively similar to those faced by scientists in other habitats, they are magnified in the coastal transition zone. The goal of this paper is to describe the difficulties that confront the researcher interested in the CTZ, and to offer some ideas for ways in which we as scientists can approach these challenges more fruitfully.