All over the world, peatlands have been drained, often for agricultural purposes, resulting in CO2 emissions, soil subsidence and biodiversity loss. To combat these negative effects, drained peatlands are being rewetted, but knowledge of the effects of rewetting on peat biogeochemistry is still incomplete, especially since a variety of rewetting methods and rewetting degrees exists. We conducted a mesocosm experiment in which we exposed 100 intact agricultural fen peat cores (80 cm, 20 cm Ø) to five different water levels (0, 20, 40, 60 cm and variable—surface), two nutrient application levels to mimic continued agricultural use, and two water origins. Over an eight-month period, we harvested above-ground plant biomass five times and sampled pore water at two depths each month. Samples were analysed for nutrients. Our results show increased phosphate and ammonium availability upon fully rewetting (0 cm—surface) and less so under partially rewetted circumstances (20 cm—surface). Above-ground biomass was strongly affected by nutrient application, especially in the high water level treatments. Vegetation was primarily N-limited, and N in the vegetation decreased with increasing water levels, indicating stronger nitrogen limitation upon rewetting. We conclude that nature restoration under fully rewetted conditions will likely be challenging as a result of the large release of nutrients from the system which may also affect surrounding nature areas. Furthermore, we conclude that partial rewetting combined with low-intensity agricultural use can be a solution to slow down the adverse effects of drainage, although this will lead to decreased agricultural production.