Francisco Rueda performed Engineering studies at the University of Cordoba (1986-1992) and obtained Extraordinary Distinction (Technical School of Agricultural and Forest Engineering, University of Córdoba) and First National Distinction in Agricultural Engineering (1993 Spanish Ministry of Education and Science) awards in recognition for outstanding academic transcript. His MSc and PhD studies were funded by fellowships from the Spanish Ministry of Education and Science in U.S.A (May, 1995 - April, 1999), and from the University of California Toxic Substances Research and Teaching program (UCTSR&TP) (July 1999 - June 2001). He obtained MSc (2000) and PhD (2001) degrees in Civil and Environmental Engineering (University of California Davis). After that, he was a Postgraduate Research Engineer (Dept. Civil & Environmental Engineering, University of California, Davis, 2001), a Visiting Postdoctoral Research Associate, Univ. of Mississipi (Oxford, 2001), and a Postdoctoral Research Associate, School of Civil & Environmental Engineering (Cornell University, 2001-2003).

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Since 2003 he is associated to the University of Granada, first as Research Associate within the Program "Ramón y Cajal" (2003-2007), and later as Assistant Professor (2007-2011), Associate Professor (2011-2017), and since 2017, as Full Professor in the Department of Civil Engineering. He teaches among others 'Environmental Engineering for Water Quality' in the Civil Engineering Program at the Univ. of Granada, "Hydrologic Processes" and "Water Quality Modelling" in the MSc Program on Technologies and Sciences for Water Quality (Univ. of Granada), or 'Simulation and Analysis of Environmental Systems' in the MSc Program on 'Ingeniero de Caminos Canales y Puertos'.

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He has served as an external reviewer for the University of California-Davis, in their internal contracting processes for research personnel. He is also a reviewer of research proposals for U.S. National Science Foundation, "Agencia Nacional de Evaluación y Prosprectiva" and "Fundación BBVA". In adittion, he is a member of the Editorial Committee of the journal LIMNÉTICA, sponsored by the Iberian Association for Limnology and indexed in the area of LIMNOLOGY in the JCR (2009-2016), and a member of the Management Committee of Lake and Reservoir Management Specialist Group del International Water Association (since 2010 a 2014). Since January 2015 until 2019, he acted as Associate Editor for LIMNOLOGY and OCEANOGRAPHY, of the Association for the Sciences of Limnology and Oceanography, a scientific journal that is ranked first in the area of LIMNOLOGY in JCR. He has chaired the Organizing Committee of the 10th International Workshop of Physical Processes in Natural Waters,Granada, June, 2006. He has also chaired the Organizing Committee of the 2nd IWA Symposium on Lake and Reservoir Management, celebrated in Granada (June 2011) and funded by "Ministerio de Ciencia e Innovación -Subprograma de Acciones Complementarias-Plan Nacional de I+D+i 2008-2011".

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Since 2002, he as edited a book, and collaborated in 6 book chapters. He has authored more than 50 JCR research articles. He has participated in more than 80 research presentations in a wide range of scientific conferences. He has presented seminars and invited speeches in several institutions including Stanford University, United States Geological Survey, or the Swiss Federal Institute for Water Science and Technology EAWAG. He has participated in 24 research projects and contracts, in 14 of them as Principal Investigator PI. He collaborates actively with highly prestigious laboratories and institutions around the world, in the area of Environmental Fluid Mechanics (UCDavis, UC-Santa Barbara, Stanford & Cornell University, Virginia Tech). He has supervised 5 doctoral dissertations at the  University of Granada, and served in the PhD Committee of three PhDs in the Universities of California-Davis, and Virginia Tech. He is one of the 'guarantors' for the area of Computational Hydraulics in the PhD program in Civil Engineering of the University of Granada. He has had five postdoctoral researchers and nearly 30 MSc students working under his supervision.

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His research is on the field of physical limnology, and aims at understanding the role of transport and mixing processes in the biogeochemical behaviour of inland water bodies.