Abstract The development and application of ecosystem models in estuarine and coastal systems has grown exponentially over the past four decades. Models have become ensconced as major tools for both heuristic study of ecosystem structure and function as well as for informing management decisions, particularly with respect to cultural eutrophication. In recent years an ever-expanding toolbox of modeling approaches is being offered to complement traditional methods. This expansion of modeling in estuarine and coastal science was exemplified by four sessions devoted to modeling at the 2007 biennial conference of the Estuarine Research Federation in Providence, RI. We felt the time was right to propose a special session of Ecological Modelling to synthesize talks from these sessions to present the state of the art in coastal and estuarine modeling. The collection of papers contained in this special issue presents a diversity of traditional and novel modeling approaches, methods for assessing model validity and predictability, and the utility of models in management applications. We believe that together these papers provide an excellent overview of current approaches to modeling estuarine hydrodynamics, water quality, and ecosystem/food web dynamics, applications of complex and relatively simple modeling approaches, applications in both deep and shallow coastal systems, goals relevant for both heuristic and management applications, and perspectives based on traditional mechanistic model development as well as more recent alternative approaches.