Mallin's current research interests include the causes and effects of eutrophication, the sources and impacts of urban pollution, land use and how it affects water quality, techniques on mitigating urban pollution, and environmental management issues. He serves as the Research Coordinator for the Lower Cape Fear River Program and the Wilmington Watersheds Program. In his research he collaborates with biologists, chemists, engineers and land use planners. His publications include studies on factors influencing bacterial contamination of coastal and inland waters, pollution from industrial scale swine and poultry farms, thenutrient and plankton ecologyof the coastal ocean, the effects of weather on ecosystems,nutrient sensitivity of streams, rivers, and estuaries, and the environmental quality of urban and rural watersheds.