This dataset contains continuous water temperature measurements collected during a controlled mesocosm experiment conducted at the AWI Sylt Outdoor Mesocosm facility, Wadden Sea Station Sylt, Germany, between June and September 2025. The experiment investigated the effects of sediment grain size, microtopography and climate warming on the salt marsh pioneer Salicornia. Plants were grown in PVC tubes filled with sandy, mixed or muddy sediments and exposed to four different climate treatments (ambient, warming, warming-drought, heatwave-drought). Climate treatments were implemented through active control of the water temperature. Experimental microtopographies simulated small-scale elevation differences. The experiment was conducted under controlled mesocosm conditions to quantify the relative importance of sediment properties, topographic variation and warming for pioneer marsh vegetation performance.