The detection, characterization and assessment of water loss through hydrological pathways is an important aspect of civil, hydrological and environmental engineering. At any site, variations in the form and hydrological integrity of both natural and man-made features can play a critical role in fluid transportation through the presence of enhanced hydraulic conductivity. Traditional hydrological and invasive engineering investigation methods are often unsuitable for ecologically sensitive environments and in this paper, we report the results of a non-invasive hydro-geophysical study at the Bosheston Lily Ponds in Pembroke, South Wales, UK, an area classified a Special Area of Conservation (SAC). For over 30 years, the lake system has experienced unexplained water loss and the geophysical surveys focused on identifying hydraulic conduits/pathways in the underlying carboniferous limestone and assessing the integrity of the man-made dam structure at the outlet of the lake system. The site is managed under tight regulatory regime that limits the scope and extent of any hydrological/geophysical investigations. The main objectives were to determine whether bedrock fracturing is promoting natural water loss and, more pertinently, if structural failures in the modern (and original) dam structures were responsible for significant loss of water at the outlet of the lakes. Ground-penetrating radar (GPR), electrical resistance tomography (ERT) and self-potential (SP) surveys were collected at targeted sites and the information gained used to ascertain the nature of the observed/predicted lake water loss. The results show that both the modern and original dam appear to be intact, structurally sound and show no evidence for significant water flow through its structures. Instead, localized zones of natural, high-density fracturing in the limestone bedrock appear to be the predominant cause of lake water loss. seasonal average. However, the summer level of the lake has systematically decreased over the last 30 years and hydrological investigations, which studied the hydrological sinks and sources of the lily ponds, concluded that a staggering 250 000 m 3 of water is lost per month through seepage and evaporation. Various explanations have been proposed for the seepage pathways with the most compelling arising from observations of water flowing into the lakeside shoreline (i.e., outward flow through natural bedrock fracture zones) and the up-welling of freshwater in front of the man-made modern dam at the seaward end of the lake. Previous hydrological investigations, including dye tracer experiments and hydrological modelling, have all been unable to identify the key hydraulic pathways and determine the major causes of lake water seepage. It has been suspected for some time that, along with natural loss (through fractures in the limestone bedrock), structural weakness in the dam at the far end of the lily pond system was responsible for a major component of the seepage. As a European Special Area of Conservation, the FIGURE 1 Lo...