This study simulated a 9-months warming scenario on the common seagrass Zostera marina from winter into summer (December 2015 - August 2016) in the Western Baltic Sea (Kiel Fijord), using outdoor mesocosms. Two treatments were applied: Ambient temperature regime (Ambient) and Ambient + 3.6C (Heat) over the entire course of the experiment. Temperature regimes were compared to the 22-year temperature average in the area. This dataset shows final above and below ground biomass per shoot for each shoot measured. The organization of the data is hierarchical: Treatment (Heat, Ambient), Benthocosms number (6 benthocosms per treatment), Seagrass box number (4 boxes per benthocosm), shoot number (originally 6 shoots per box, some were lost throughout the experiment). Unit of biomass is g dry weight per shoot.