Obtained BSc and MSc degrees from the University of Malta, and a PhD degree from the University of Plymouth (UK).

His teaching interests are in the areas of animal biology, ecology and marine biology. His research activities mainly focus on ecological assessment and monitoring, with particular emphasis on themes concerning marine ecology. He is involved in research on the ecology of seagrass and algal habitats, and on the environmental impacts of aquaculture. He has been carrying out marine environmental surveys since 1991, using scientific diving and other in situ survey techniques, as well as remote sensing procedures. He leads a team of researchers at the Laboratory of Ecological Assessment and Monitoring within the Department of Biology, University of Malta.

He is fellow of three UK societies: Institute of Biomedical Science, Royal Society of Biology, and the Marine Biological Association. He publishes regularly (see publications at https://www.researchgate.net/profile/Joseph_A_Borg and https://scholar.google.com/citations?user=7qphHQwAAAAJ&hl=en&oi=ao) and acts as reviewer for several leading international marine biology journals, including 'Aquaculture Environment Interactions' for which he is Review Editor.