In 2004 the Australian Government implemented a revised zone-based management plan for the Great Barrier Reef World Heritage Area to increase protection of representative areas while minimising the impacts to the economic viability of important industries. In this study we evaluated the current zoning plan for its capacity to protect marine turtles from commercial trawling and netting activities at nesting sites and at inshore and offshore foraging areas to assess whether the Great Barrier Reef Marine Park Authority met their obligations under the Representative Areas Program (RAP). We found that protection from commercial fisheries increased within 5- and 10-km buffer zones of all very-high, high- and medium-priority nesting sites that were previously less than 100% protected. However, three very-high-priority sites and six high-priority sites remain less than 100% protected out to 5 km, falling short of the objectives of the RAP. There were variable increases in protection at foraging areas; however, each of them increased in the proportion of area protected from commercial fishing, fulfilling the objectives of the RAP. By using a broader-scale fisheries by-catch dataset as a proxy for turtle abundance we found that improvements in protection are not species-specific and can be attributed to the step-wise increases in protection since the mid 1990s.