- Ghezzo, M., De Pascalis, F., Umgiesser, G., Zemlys, P., Sigovini, M., Marcos, C. & Pérez-Ruzafa, A., 2014. Connectivity in three European coastal lagoons. Estuaries and Coasts

- García-Sánchez, M., Korbee, N., Pérez-Ruzafa, I.M., Marcos, C., López-Figueroa, F. & Pérez-Ruzafa, A., 2014. Living in a coastal lagoon environment: Photosynthetic and biochemical mechanisms of key marine macroalgae. Marine Environmental Research, 101: 8-21.

- Pérez-Ruzafa, A., Marcos, C., Pérez-Ruzafa, I.M. & Pérez-Marcos, M., 2013. Are coastal lagoons physically or biologically controlled ecosystems? Revisiting r vs. K strategies in coastal lagoons and estuaries. Estuarine, Coastal and Shelf Science, 132: 17-33.

- García-Sánchez, M., Pérez-Ruzafa, I.M., Marcos, C. & Pérez-Ruzafa, A., 2012. Suitability of benthic macrophytes indices (EEI, E-MaQI and BENTHOS) for detecting anthropogenic pressures in a Mediterranean coastal lagoon (Mar Menor, Spain). Ecological Indicators, 19: 48-60.

- García-Sánchez, M., Korbee, N., Pérez-Ruzafa, I.M., Marcos, C., Domínguez, B., López-Figueroa, F. & Pérez-Ruzafa, A., 2012. Physiological response and photoacclimation capacity of Caulerpa prolifera (Forsskål) J.V. Lamouroux and Cymodocea nodosa (Ucria) Ascherson meadows in the Mar Menor lagoon (SE Spain). Marine Environmental Research, 79: 37-47.

- De Pascalis, F., Pérez-Ruzafa, A., Gilabert, J., Marcos, C. & Umgiesser, G., 2012. Climate change response of the Mar Menor coastal lagoon (Spain) using a hydrodynamic finite element model. Estuarine, Coastal & Shelf Science, 114: 118-129.

- Franco, A., Pérez-Ruzafa, A., Drouineau, H., Franzoi, P., Koutrakis, E.T., Lepage, M., Verdiell-Cubedo, D., Bouchoucha, M., López-Capel, A., Riccato, F., Sapounidis, A., Marcos, C., Oliva-Paterna, F.J., Torralva-Forero, M. & Torricelli, P., 2012. Assessment of fish assemblages in coastal lagoon habitats: Effect of sampling method. Estuarine, Coastal & Shelf Science, 112: 115-125.

- Pérez-Ruzafa, A., Marcos, C., Bernal, C.M., Quintino, V., Freitas, R., Rodrigues, A.M., García-Sánchez, M. & Pérez-Ruzafa, I.M., 2012. Cymodocea nodosa vs. Caulerpa prolifera: Causes and consequences of a long term history of interaction in macrophyte meadows in the Mar Menor coastal lagoon (Spain, southwestern Mediterranean). Estuarine, Coastal & Shelf Science, 110: 101-115.

- Pérez-Ruzafa & Marcos, C., 2012. Fisheries in coastal lagoons: An assumed but poorly researched aspect of the ecology and functioning of coastal lagoons. Estuarine, Coastal & Shelf Science, 110: 15-31.

- Pérez-Ruzafa, A., Marcos, C. & Pérez-Ruzafa, I.M., 2011. Recent advances in coastal lagoons ecology: evolving old ideas and assumptions. Transitional Waters Bulletin, 5 (1): 50-74. http://siba-ese.unisalento.it/index.php/twb/article/view/12306

- Pérez-Ruzafa, A., Marcos, C., Pérez-Ruzafa, I.M. & Pérez-Marcos, M., 2011. Coastal lagoons: “transitional ecosystems” between transitional and coastal waters. Journal of Coastal Conservation, 15: 369-392.

- Pérez-Ruzafa, A., Marcos, C & Pérez-Ruzafa, I.M., 2011. Mediterranean coastal lagoons in an ecosystem and aquatic resources management context. Physics and Chemistry of the Earth, 36: 160-166.

- García-Sánchez, M., Korbee, N., Pérez-Ruzafa, I.M., Marcos, C., Navarro, N., Jofre, J., Domínguez, B., Pérez-Ruzafa, A. & López-Figueroa, F., 2011. Physiological adaptations of macrophytes key species to coastal lagoons in a climate change scenario. European Journal of Phycology, 46(SI): 149-150.

- Pérez-Ruzafa, A., Marcos, C. & Pérez-Ruzafa, I.M., 2009. 30 años de estudios en la laguna costera del Mar Menor: de la descripción del ecosistema a la comprensión de los procesos y la solución de los problemas ambientales. En: Instituto Euromediterráneo del Agua (Ed.), El Mar Menor. Estado actual del conocimiento científico. Fundación Instituto Euromediterráneo del Agua, Murcia: 17-46.

- Pérez-Ruzafa, A., Hegazi, M.I., Pérez-Ruzafa, I.M. & Marcos, C., 2008. Differences in spatial and seasonal patterns of macrophyte assemblages between a coastal lagoon and the open sea. Marine Environmental Research, 65: 291-314.

- Pérez-Ruzafa, A. & Marcos, C., 2008. Coastal lagoons in the context of water management in Spain and Europe. En: Gönenc, I.E., Vadineanu, A., Wolflin, J.P. & Russo, R.C. (Eds.) Sustainable Use and Development of Watersheds. NATO Science for Peace and Security Series. Springer: 299-321.

- Pérez-Ruzafa, A., Marcos, C., Pérez-Ruzafa, I.M., Barcala, E., Hegazi, M.I. & Quispe, J., 2007. The problem of detecting changes under human pressure in a naturally quick-changing and heterogeneous environment: spatial and temporal scales of variability in coastal lagoons. Estuarine, Coastal and Shelf Science, 75: 175-188.

- Pérez-Ruzafa, A., Mompeán, M.C. & Marcos, C., 2007. Hydrographic, geomorphologic and fish assemblage relationships in coastal lagoons. Hydrobiologia, 577: 107-125.

- Pérez-Ruzafa, A., García-Charton, J.A., Barcala, E. & Marcos, C., 2006. Changes in benthic fish assemblages as a consequence of coastal works in a coastal lagoon: The Mar Menor (Spain, Western Mediterranean). Marine Pollution Bulletin, 53: 107-120.

- Pérez-Ruzafa, A., Fernández, A.I., Marcos, C., Gilabert. J., Quispe, J.I. & García-Charton, J.A., 2005. Spatial and temporal variations of hydrological conditions, nutrients and chlorophyll a in a Mediterranean coastal lagoon (Mar Menor, Spain). Hydrobiologia, 550: 11-27.

- Salas, F., Marcos, C., Pérez-Ruzafa, A. & Marques, J.C., 2005. Application of the exergy index as ecological indicator of organically enrichment areas in the Mar Menor lagoon (south-easthern Spain). Energy, 30: 2505-2522.

- Gamito, S., Gilabert, S., Marcos, C. & Pérez-Ruzafa, A., 2005. Effects of Changing Environmental Conditions on Lagoon Ecology. En: Gönenç, I.E. & Wolflin, J.P. (Eds.), Coastal Lagoons: Ecosystem Processes and Modeling for Sustainable Use and Development. CRC Press, Boca Ratón, Florida: 193-229.

- Pérez-Ruzafa, A., Marcos, C. & Gilabert, J., 2005. The ecology of the Mar Menor coastal lagoon: a fast-changing ecosystem under human pressure. En: Gönenç, I.E. & Wolflin, J.P. (Eds.), Coastal Lagoons: Ecosystem Processes and Modeling for Sustainable Use and Development. CRC Press, Boca Ratón, Florida: 392-422.

- Pérez-Ruzafa, A. & Marcos, C., 2005. Pressures on Mediterranean coastal lagoons as a consequence of human activities. En: Fletcher, C., Spencer, T., Da Mosto, J. & Campostrini, P. (Eds.), Flooding and Environmental Challenges for Venice and its Lagoon: State of Knowledge. Cambridge University Press, Cambridge: 545-555.

- Pérez-Ruzafa, A., Mompeán, M.C. & Marcos, C., 2005. To what extent ecological information can be explained by geomorphological characteristics of coastal lagoons? In: Lasserre, P., Viaroli, P. & Campostrini, P. (Eds.), Lagoons and Coastal Wetlands in the Global Change Context: Impacts and Management Issues. ICAM Dossier Nº 3, UNESCO: 62-69.

- Pérez-Ruzafa, A., Quispe-Becerra, J.I., García-Charton, J.A. & Marcos, C., 2004. Composition, structure and distribution of the ichthyoplankton in a Mediterranean coastal lagoon. Journal of Fish Biology, 64: 1-17.

- Pérez-Ruzafa, A. & Marcos, C., 2003. El Mar Menor. En: Esteve, M.A., Lloréns, M. & Martínez Gallur, C. (Eds.), Los recursos naturales de la Región de Murcia. Un Análisis interdisciplinar. Servicio de Publicaciones de la Universidad de Murcia: 404-411.

- Pérez-Ruzafa, A., Gilabert. J., Gutiérrez, J.M., Fernández, A.I., Marcos, C. & Sabah, S., 2002. Evidence of a planktonic food web response to changes in nutrient input dynamics in the Mar Menor coastal lagoon, Spain. Hydrobiologia, 475/476: 359-369.

- Pérez-Ruzafa, A., Navarro, S., Barba, A., Marcos, C., Camara, M.A., Salas, F. & Gutierrez, J.M., 2000. Presence of pesticides throughout trophic compartments of the food web in the Mar Menor lagoon (SE of Spain). Marine Pollution Bulletin, 40 (2): 140-151

- Pérez-Ruzafa, A. & Marcos, C., 1993. La teoría del confinamiento como modelo para explicar la estructura y zonación horizontal de las comunidades bentónicas en las lagunas costeras. Publ. Espec. Inst. Esp. Oceanogr., 11: 347-358.

- Pérez-Ruzafa, A. & Marcos, C., 1992. Colonization rates and dispersal as essential parameters in the confinement theory to explain the structure and horizontal zonation of lagoon benthic assemblages. Rapp. Comm. int. Mer Medit., 33: 100.

- Pérez-Ruzafa, A., Marcos, C. & Ros, J., 1991. Environmental and Biological Changes Related to Recent Human Activities in the Mar Menor. Marine Pollution Bulletin, 23: 747-751.

- Pérez-Ruzafa, A., Ros, J.D., Marcos, C., Perez Ruzafa, I.M. & Ballester, R., 1989. Distribution and biomass of the macrophyte beds in a hypersaline coastal lagoon (the Mar Menor, SE Spain) and its recent evolution following major environmental changes. In: Boudouresque, Ch.-F., Meinesz, A., Fresi, E. & Gravez, V. (Eds.), International Workshop on Posidonia Beds, 2: 49-62. G.I.S. Posidonie Publisher, Marseille.

- Pérez-Ruzafa, A., Perez Ruzafa, I.M., Marcos, C. & Ros, J.D., 1988. Cartografía bionómica del poblamiento bentónico de las islas del Mar Menor, I: islas Perdiguera y del Barón. Oecologia aquatica, 9: 27-40.

- Pérez-Ruzafa, A., Marcos, C., Perez Ruzafa, I.M. & Ros, J.D., 1987. Evolución de las características ambientales y de los poblamientos del Mar Menor (Murcia, SE de España). Anales de Biología, 12 (Biología Ambiental, 3): 53-65.

- Pérez-Ruzafa, A. & Marcos, C., 1987. Los sustratos arenosos y fangosos del Mar Menor (Murcia), su cubierta vegetal y su posible relación con la disminución del mújol en la laguna. Cuadernos Marisqueros Publ. Téc., 11: 111-123.

- Ros, J.D., Pérez-Ruzafa, A., Marcos, C. & Perez Ruzafa, I.M., 1987. Resultados preliminares en el estudio del bentos del Mar Menor. Cuadernos Marisqueros Publ. Téc., 11: 305-321.

- Departamento de Ecologia, Universidad de Murcia, 1985. Estudio sobre aumento de la producción pesquera en el Mar Menor. Cámara de Comercio, Industria y Navegación de Murcia. 160 pp.