- Gonçalves A.M.M., Mesquita A.F., Verdelhos T., Coutinho J.A.P., Marques J.C., Gonçalves F. (2016). Fatty acids’ profiles as indicators of stress induced by of a common herbicide on two marine bivalves species:Cerastoderma edule (Linnaeus, 1758) and Scrobicularia plana (da Costa, 1778). Ecological Indicators, 63: 209-218.
- Martins I., M.R. Flindt, M.A. Pardal, A.I. Lillebø, J.M. Oliveira, J.C. Marques (2002). Nutrient dynamics in the intertidal pools of the Mondego estuary. III- The importance of nutrient effluxes to macroalgal growth (Enteromorpha sp.). In Pardal M. A., Marques J. C. & Graça M. A. S. (eds) Aquatic ecology of the Mondego river basin. Global importance of local experience. Chapter 3.4: 273-286, Imprensa da Universidade de Coimbra, Coimbra.
- Martins I., Lopes R.J., Lillebø A.I., Neto J.M., Pardal M.A., Ferreira J.G., Marques J.C. (2007). Significant variations in the productivity of green macroalgae in a mesotidal estuary: Implications to the nutrient loading of the system and the adjacent coastal area. Marine Pollution Bulletin, 54: 678-690.
- Teixeira H., Neto J.M., Patrício J., Veríssimo H., Pinto R., Salas F., Marques J.C. (2009). Quality assessment of benthic macroinvertebrates under the scope of WFD using BAT, the Benthic Assessment Tool. Marine Pollution Bulletin, 58: 1477-1486.
- Teixeira Z., Marques J.C. (2016). Relating landscape to stream nitrate-N levels in a coastal eastern-Atlantic watershed (Portugal). Ecological Indicators, 61 (part 2): 693-706.
- Veríssimo H., Bremner J., Garcia C., Patrício J., van der Linden P., Marques J.C. (2012). Assessment of the subtidal macrobenthic community functioning of a temperate estuary following environmental restoration. Ecological Indicators, 23: 312-322.
- Vinagre P.A., Pais-Costa A.J., Marques J.C., Neto J.M. (2015). Setting reference conditions for mesohaline and oligohaline macroinvertebrate communities sensu WFD: Helping to define achievable scenarios in basin management plans. Ecological Indicators, 56: 171-183.