The data set describes the effects of three neonicotinoid seed treatments (clothianidin, thiamethoxam and a control) applied to winter sown oilseed rape in Hungary, Germany and the UK on honeybees (Apis mellifera). The data describes population responses in terms of European Food Safety Authority (EFSA) primary (colony strength and overwintering success) and secondary assessment endpoints for the response of honeybees to exposure to the neonicotinoids. Information on expression of neonicotinoids in the pollen and nectar from the crop or collected by bees is also included, as well as details of honeybee diseases and foraging preferences. This research was undertaken by the Centre for Ecology & Hydrology in 2015 and was funded by Syngenta Ltd. and Bayer CropScience.