Mercury concentrations in the atmosphere, surface waters, and soils have increased beyond natural levels as a result of human activities, which poses a risk to human and environmental health. Ireland is situated on the western periphery of Europe, and it is generally assumed that environmental mercury is low but there is limited information on mercury within natural environments. In this study, the interlinkages in the concentration of mercury in soils, lake sediment, and lake water were investigated in remote upland acid-sensitive catchments influenced by low deposition of atmospheric mercury. Thirty-one upland lake catchments were sampled for topsoil, lake sediment, and lake water during 2017–2018. Total mercury (THg) concentrations in water (median 5.4 ng/L) and sediment (median 30 ng/g) were low, owing to the remote location of the lakes. In contrast, THg in catchment soil was relatively high for a background region (median: 240 ng/g), which was attributed to the high organic matter content of the soil (median 87%). The results suggest catchment soils are the dominant driver of variation in THg in lake water and sediment in upland regions in Ireland. Further, given that highly organic soils can obscure interlinkages within catchments, this study demonstrated the value of exploring mercury independent of the influence of organic matter, i.e., THg normalized by organic carbon. As global action (such as the Minamata Convention) decreases mercury emissions, legacy soil mercury may become a more important input to aquatic systems than atmospheric deposition, which makes the relationships between terrestrial catchments and their water bodies vital for our understanding of mercury cycling.