In 2004 Chaplin was invited by a group of scientists from his father’s old institution, The Academy of Natural Sciences in Philadelphia, to participate in a 50-year retrospective study of the coral reef environment he’d frequented as a child, using his father's work as a baseline. His article "Return to the Reefs,"  and his subsequent book "Full Fathom Five: Ocean Warming and a Father’s Legacy" (Skyhorse Publishing, 2013)  are accounts of this effort. As a research associate at the Academy, he is a co-author of two resulting scientific studies, "Assessing 50-year changes in Bahamian Reef Fish Assemblages: Evidence for Community Response to Recent Disturbances?" and "Detection of Shifts in coral reef fish assemblages structures over 50 years at reefs of New Providence Island, the Bahamas, highlights the value of the Academy of Natural Sciences collections in a changing world". In 2009 he established the Chaplin Fellowship at the Academy of Natural Sciences, occupied by Dr. Katriina Ilves. Chaplin's most recent book is another novel, Paraíso (Skyhorse Publishing, 2016) set in Todos los Santos, about a gringo brother and sister who whose long estrangement ends in a spectacular rescue. Chaplin lives in New York City and Hebron, New York, with his wife Sarah Teale and daughter Rosie. In Hebron they run a grass-fed beef operation, Rosie’s Beef, and are putting together a farmers co-operative for marketing farm to table production. Chaplin has two daughters from a previous marriage, Diana and Julia.