[4] Her masterate research, supervised by Patricia Bergquist, was an investigation of the systematics and ecology of the sponges of Motupore Island in Papua New Guinea.
[4][5] She then earned a PhD at the University of Auckland in 1991 under the joint supervision of Patricia and Peter Bergquist, with a thesis entitled, The order Hadromerida (Porifera: Demospongiae), taxonomy and relationships of the major families,[6] and in the same year (with Patricia Bergquist) published a paper on the genus, Tethya.
[7] From 1991 to 1992, Kelly was a post-doctoral fellow at the Florida Atlantic University Harbor Branch Oceanographic Institute, working with Shirley A. Pomponi, studying natural products extracted from deep-sea sponges and analysing DNA sequences.
[10] From 1993, she spent four years with the Natural History Museum, London, carrying out research on sponges in the Indo-Pacific,[4][11] before returning to New Zealand and working as a senior scientist in the Department of Landscape and Plant Science at Unitec Institute of Technology in Auckland and a consultant to the Coral Reef Research Foundation in Micronesia.
In 2011, Kelly was awarded the degree of Doctor of Science by the University of Auckland, on the basis of her papers published since 1988 on the taxonomy, systematics and phylogeny of sponges.