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 continues temperature data for each benthocosm and the adjacent fjord. Benthocosms A1, A2, C1, C2, E1, E2 = Heat; Benthocosms B1, B2, D1, D2, F1, F2 = Ambient.