Martins research focuses on the two-way linkage between environmental change and ecosystems. He centres on the following components of the environmental cause-effect chain: land use and water management -> water fluxes, water quality and biogeochemical cycles -> ecosystem functioning and biodiversity. Human intervention affects the hydrological cycle and elemental cycles with associated effects on pools, fluxes and transport of water and elements and the dynamics of resource limitation. The cumulative effects of such changes on the resilience of species, inter-specific competition and species migration and adaptation, and how this affects ecosystem functioning are key issues in his research. Apart from impact studies of (global) change on ecosystems and species, he also analyses how terrestrial and wetland ecosystems feedback to global cycles of water, carbon and nutrients. Some of his projects address typical nature conservation issues such as landscape ecological relations of nature areas with the larger scale landscape, water management of wetlands, nutrient-management, re-introduction of large herbivores, novel ecosystems.    

Martin considers environmental sciences as an interdisciplinary science in which integration of disciplines is brought about; each with its own research questions and methods but mutually starting from a joint problem definition and synthesizing in trying to understand the role of man in a changing world. Such cooperation in multi-disciplinary teams gives a great added value as is demonstrated by the societal relevance of his research. His research develops and uses models and also generates indicators for environmental quality determined in pristine ecosystems.