Technical advances in monitoring devices are allowing managers and scientists to obtain quality information on ecosystem health with minimal disturbance to ecosystems and the wildlife they support. We rely on temporal and spatial indicators of ecosystem health, such as population abundance estimates, to understand and predict ecosystem change. This is critical for the achievement of conservation goals while supporting sustainable natural resource use. Obtaining abundance estimates can be logistically demanding and expensive particularly in offshore marine environments, and for some species, can cause significant disturbance. These constraints may lead to sub-optimal monitoring programs that reduce the frequency and/or precision of surveys at the cost of data quality or power in the resulting analyses. Using unpiloted aerial vehicles (UAVs) can be a solution to this dilemma and can improve the accuracy of estimates. With appropriate testing and ethical consideration; for many situations, UAVs can increase the frequency of surveys and enable more robust and reliable programs for monitoring ecosystem health. In this talk we demonstrate the process of testing and calibrating a UAV for monitoring abundance and body size of Australian fur seals at their largest colony. Two sizes of quadcopter with different gear at various altitudes above sea level were tested. We assessed disturbance levels in the seals and birds and optimised a methodology that allows effective and economical monitoring of this site. The benefits and disadvantages of such an approach will be outlined, as well as important considerations for those looking to incorporate similar methodologies in their research.