Ambient water temperature is a key factor controlling the distribution and impact of disease in fish populations, and optimum temperature ranges have been characterised for the establishment of a number important aquatic diseases exotic to the UK. This study presents a simple regression method to approximate daily average surface water temperature in lakes of 0.5–15 ha in size across the UK using 5 km2 gridded daily average air temperatures provided by the UK Meteorological Office. A Geographic information system (GIS) is used to present thematic maps of relative risk scores established for each grid cell based on the mean number of days per year that water temperature satisfied optimal criteria for the establishment of two economically important pathogens of cyprinid fish (koi herpesvirus (KHV) and spring viraemia of carp virus (SVCV)) and the distribution and density of fish populations susceptible to these viruses. High-density susceptible populations broadly overlap the areas where the temperature profiles are optimal for KHV (central and south-east England); however, few fish populations occur in areas where temperature profiles are most likely to result in the establishment of spring viremia of carp (SVC) (namely northern England and Scotland). The highest grid-cell risk scores for KHV and SVC were 7 and 6, respectively, out of a maximum score of 14. The proportion of grid cells containing susceptible populations with risk scores of 5 or more was 37% and 5% for KHV and SVC, respectively. This work demonstrates a risk-based approach to inform surveillance for exotic pathogens in aquatic animal health management, allowing efficient use of resources directed towards higher risk animals and geographic areas for early disease detection. The methodology could be used to examine the change in distribution of high-risk areas for both exotic and endemic fish diseases under different climate change scenarios.