The dataset contains instantaneous fluxes of carbon dioxide, methane and nitrous oxide from intact lysimeters in agricultural grasslands in the Hampshire Avon catchment (UK). Manipulations of soil temperature, soil water saturation, additions of nitrogen, phosphorus and of nitrogen and phosphorus were made at three orthogonal experiments in three sub-catchments of contrasting geology (chalk, clay and greensand). Fluxes of carbon dioxide were directly measured continuously during 2014 and 2015 using automated chamber approach, and fluxes of methane and nitrous oxide were measured in 'campaign' mode. Flux measurements consisted of chamber closure for 180 seconds, except when in 'campaign' mode when measurement periods were extended to 300 seconds.