Climate-driven sea level rise has severe consequences for drained agricultural areas near coasts. The least productive of these can be restored into marine wetlands of high ecological quality by managed realignment. This study assessed the nitrogen (N) and phosphorus (P) balance in a 214 ha coastal lagoon formed after flooding of agricultural land by managed realignment. N and P loss from the soils was monitored over a 5-year period after flooding using three independent approaches: (1) temporal changes in N and P inventories of the soil; (2) flux of dissolved inorganic N and P from the flooded soil; and (3) tidal N and P exchange across the outer boundary in the form of particulate and dissolved nutrients. All three approaches showed similar initial release and tidal export of N and P the first year(s) after flooding followed by decreasing rates. The annual loss ranged from 157 to 299 kg N ha−1 yr−1 and 29 to 63 kg P ha−1 yr−1 during the first year. N loss decreased rapidly after the first 2 years and reached a level of 28–65 kg N ha−1 yr−1, while P loss declined after the first year and remained stable and relatively high at 18–32 kg P ha−1 yr−1 thereafter. High N and P export after implementing managed realignment of agricultural land may deteriorate environmental conditions in the adjacent marine recipients for at least 5 years. Particularly small and stagnant water bodies vulnerable to eutrophication should be avoided as recipients.