He is Full Professor at the Department of Zoology at the Faculty of Science and Technology of the University of Coimbra. He was Vice-President for Scientific Research of the University of Coimbra and and President of the Scientific Commission of the Zoology Department of the same institution. His academic interests include mainly research into biological and ecological processes of marine and estuary eco-systems and the ecology of systems. Particularly noteworthy amongst his published work are the following: "Analysis of the properties of exergy and biodiversity along an estuarine gradient of eutrophication. Ecological Modelling", Marques, J. C., M. A. Pardal, S. N. Nielsen & S. E. Jørgensen, 102:155-167, 1997; "Three selected ecological observations interpreted at the light of a thermodynamic hypothesis. A contribution to a general ecological theoretical network. Ecological Modelling", Marques, J. C. & S. E. Jørgensen158: 213-221, 2002; "Impact of eutrophication and river management within a framework of ecosystem theories. Ecological Modelling", Marques, J. C., S. N. Nielsen, M. A. Pardal & S. E. Jørgensen, 166 (1-2): 147-168, 2003; "Comparison of Talitrus saltator (Amphipoda, Talitridae) biology, dynamics, and secondary production in Atlantic (Portugal) and Mediterranean (Italy and Tunisia) populations. Estuarine Coastal and Shelf Science", Marques, J. C., S. C. Gonçalves, M. A. Pardal, L. Chelazzi, I. Colombini, M. Fallaci, M. F. Bouslama, M. El Gtari, F. Charfi-Cheikhrouha & F. Scapini, 58 S : 127-148, 2003; "Application of ecological indicators to assess environmental quality in coastal zones and transitional waters. Two case studies", Marques, J. C., F. Salas, J. M. Patrício, and M. A. Pardal. In S.E. Jørgensen, R. Costanza & X. Fu-Liu (eds) Handbook of ecological indicators for assessment of ecosystem health. CRC Press, pp 67-104, 2005.