The main strength of WBI's research program is its emphasis on wetland biogeochemical processes combined with a multi disciplinary approach to studying wetlands. WBI's research in wetlands includes coastal wetland loss, marsh accretion and stability, investigations of redox chemistry of wetlands, the role of wetlands in global biogeochemical cycles (C, N, S, P, O), sedimentation processes, environmental chemistry of toxic metals and organics, soil morphology and water quality functions, greenhouse gas production and emission, biotic and abiotic controls on wetland plant growth and distribution, wetland plant stress physiology and adaptations, effects of global change factors on wetland vegetation, and ecosystem ecology.

In addition to this strong, basic research program, the institute also conducts projects with more applied objectives such as wetland restoration, oil bioremediation, improvement of yields in agricultural wetlands, treatment of industrial and municipal wastes, and functional assessment and delineation of freshwater wetlands.

The Institute also has an international research program pertaining to the biogeochemistry wetland ecosystems throughout Latin America and Asia, including mangroves and rice-paddy soils.