<p>Peat decomposition in managed peatlands is responsible for a decrease of 0.52 GtC yr<sup>−1</sup> in global carbon stock and is strongly linked to drainage to improve the agricultural bearing capacity, which increases aeration of the soil. Microbial aerobic decomposition is responsible for the bulk of the net CO<sub>2</sub> emission from the soil and could be reduced by wetting efforts or minimizing drainage. However, the effects of rewetting efforts on microbial respiration rate are largely unknown. We aimed to obtain more insight in these rewetting effects and measured them for 1 year for two dairy farming peatlands where submerged drainage subsurface irrigation (SDSI) was tested against a control situation. With a modelling approach, we explored the effects of rewetting under different weather conditions, water management strategies (raising ditch water levels and SDSI) and hydrological settings. We introduced a methodology to estimate potential aerobic microbial respiration rate as measure for peat decomposition in managed peatlands, based on potential respiration rate curves for soil temperature and water filled pore space (WFPS). Rewetting with SDSI resulted in higher summer groundwater levels, soil temperatures and WFPS. SDSI reduced net ecosystem production (NEP) with 1.27 ± 0.39 kg CO<sub>2</sub> m<sup>−2</sup> yr<sup>−1</sup> (83 %) and 0.78 ± 0.37 kg CO<sub>2</sub> m<sup>−2</sup> yr<sup>−1</sup> (35 %) for Assendelft and Vlist respectively. With the process based modelling approach we found that raising ditch water levels always reduces peat respiration rates. Furthermore, we found that the application of SDSI reduces yearly peat respiration rates in environments in a dry year and/or with downward hydrological fluxes, and increases peat respiration rates in a wet year and/or when upward groundwater fluxes are present. Moreover, combining SDSI with high ditch water levels or pressurizing SDSI systems will further reduce peat respiration rates. We highly recommend to use a process-based approach based on temperature and WFPS soil conditions to determine effectivities of rewetting efforts over empirical relationships between average groundwater level and NEP. Such a more process based approach allows to distinguish between groundwater levels raised by SDSI and ditch water levels. When this is not possible, we recommend using mean summer groundwater level instead of mean annual groundwater level as a proxy to estimate NEP. Such relations between mean groundwater levels and NEP need to be corrected for situations with SDSI.</p>