Floating covers are examples of a large membrane structure used at sewage treatment plants. At the Western Treatment Plant (WTP), Werribee, Melbourne, Australia, floating covers are used in the anaerobic lagoons. They are deployed to assist with the anaerobic treatment of the raw sewage beneath, to harness the methane-rich biogas generated and for odour control. In this respect, these floating covers are important assets for harnessing a sustainable and renewable energy source, as well as protecting the environment from the release of the damaging greenhouse methane-rich biogas from the treatment plant. Given the continuous nature of the biological process beneath the cover, the forces imposed on the floating cover will change with time. Hence, the monitoring and assessment of the structural integrity of the floating cover are of paramount importance. These floating covers are made from high density polyethylene (HDPE), a polymeric material. The size of these covers, the hazardous environment and the expected life span, demand a novel, remotely piloted, unmanned aerial vehicle based non-contact technique for structural health assessment. This assessment methodology will utilise photogrammetry as the basis for determining the surface deformation of the membrane. This paper reports on an experimental study to determine the flight parameters and to assess the accuracy of the measurement technique. It was conducted over an area having similar dimensions to the large covers at the WTP. There are also features in this area which are of similar scale to those expected in the floating cover. A total of nine test flights was used to investigate the parameters for optimal definition of the significant features to describe the deformation of the floating cover. The findings inform the selection of the unmanned aerial vehicle assisted photogrammetry parameters for optimal flight altitude, photogrammetry image overlap, and flight grid path for future integrity assessment of the floating covers. Two trial flights at WTP are also discussed to demonstrate the effectiveness of this non-contact technique for future structural health assessment and in assisting with the operation of this large high-value asset.