For many marine megavertebrate species it is challenging to derive population estimates and knowledge on habitat use needed to inform conservation planning. For marine turtles, the logistics required to undertake comprehensive ground-based censuses, across wide spatial and temporal scales, are often insurmountable. This frequently leads to an approach where a limited number of index nesting beaches are monitored in great detail by foot. In this study we use nationwide aerial surveying interfaced with ground assessments across three seasons of leatherback turtle nesting in Gabon (Equatorial West Africa), highlighting the importance of a synoptic approach to marine turtle monitoring. These surveys allow the first complete population assessment of this nesting aggregation to be made, identifying it as the world’s largest for the species (36,185–126,480 clutches, approximating to 5865–20,499 breeding females per annum and a total estimate of 15,730 to 41,373 breeding females). Our approach also serendipitously provides insights into the spatial appropriateness of Gabon’s protected areas network, for example (mean ± 1SD) 79 ± 6% (range 67–86%) of leatherback turtle activities recorded during aerial surveys (n = 8) occurred within protected areas (345 km, 58%, of surveyed coastline). We identify and discuss sources of potential error in estimating total nesting effort from aerial surveying techniques and show that interannual variation in nesting is considerable, which has implications for the detection of statistically significant changes in population size. Despite its relative costliness per day, aerial surveying can play an important role in providing estimates of relative population abundance of large vertebrates dispersed over extensive areas. Furthermore, it can provide data on habitat use and deliver real-time information on the spatial efficacy of protected area networks.