1.Projected sea-level rise (SLR) is expected to cause shoreline erosion, saline intrusion into the water table and inundation and flooding of beaches and coastal areas. Areas most vulnerable to these physical impacts include small, tropical low-lying islands, which are often key habitat for threatened and endemic species, such as sea turtles.2.Successful conservation of threatened species relies upon the ability of managers to understand current threats and to quantify and mitigate future threats to these species. This study investigated how sea-level rise might affect key rookeries (nesting grounds) (n=8) for the northern Great Barrier Reef (nGBR) green turtle population, the largest green turtle population in the world.3.3-D elevation models were developed and applied to three SLR scenarios projected by the IPCC 2007 and an additional scenario that incorporates ice melting. Results indicate that up to 38% of available nesting area across all the rookeries may be inundated as a result of SLR.4.Flooding, as a result of higher wave run-up during storms, will increase egg mortality at these rookeries affecting the overall reproductive success of the nGBR green turtle population. Information provided will aid managers to prioritize conservation efforts and to use realistic measures to mitigate potential SLR threats to the nGBR green turtle population. Copyright © 2009 John Wiley & Sons, Ltd.