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 monthly or bi-monthly measurements taken of each shoot: Number of shoots [no. per box], Number of new shoots at counting event [no. per box], number of new shoots per month [no. per box per month], and number of flowering shoots [no. per box]. Derived data in %: Number of shoots [% of original shoots], number of new shoots [% of original shoots], number of flowering shoots [% of original shoots]. 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).