This data set consists of freshwater pond quality data for sites across Wales between 2013 and 2016. Data include macrophyte species records, chemistry and water quality metrics, and environmental variables such as pollution, grazing and management from surveyed ponds. Ponds were surveyed within a set of up to 300 x 1km squares across Wales (not all sites contained pond features), collected as part of the Glastir Monitoring and Evaluation Programme (GMEP). The monitoring programme was set up by the Welsh Government in 2013 to monitor the effects of the Glastir agri-environment scheme on the environment and ran from 2013 to 2016. The field survey element was based on a stratified random sampling design of 300 x 1km square sites across Wales, and was managed by the UK Centre for Ecology & Hydrology.