Encouraging adaptation is an essential aspect of the policy response to climate change. However, given that human activities are the main cause of environmental transformations worldwide, it follows that adaptation itself has the potential to generate further pressures, creating new threats for both local and global ecosystems. From this perspective, policies designed to encourage adaptation may conflict with regulation aimed at preserving or enhancing environmental quality. This aspect of adaptation has received relatively little consideration in either policy design or academic debate. To highlight this issue, the authors analyse the trade-offs between two fundamental ecosystem services which will be impacted by climate change: provisioning services derived from agriculture and regulating services in the form of freshwater quality. Their results indicate that climate adaptation in the farming sector will generate fundamental changes in river water quality. In some areas, policies which encourage adaptation are expected to conflict with existing regulations aimed at improving freshwater ecosystems. These findings illustrate the importance of anticipating the wider impacts of human adaptation to climate change when designing environmental policies.