Managed realignment by deliberate flooding of coastal areas is an adaptation to sea level rise but may risk enriching the coastal zone with nutrients when seawater floods agricultural soil. This study focuses on the early development of macroalgae and their sources of nitrogen (N) in Gyldensteen Coastal Lagoon, Denmark. The lagoon was claimed for agricultural purposes in 1871 and reflooded by managed realignment 143 yr later (2014). Our hypotheses were: (1) that nutrients of agricultural origin from the newly flooded soil initiate opportunistic macroalgal blooms; and (2) that the isotopic composition of green algae rapidly reflects the origin of nutrient sources. We monitored macroalgal cover and conducted stable isotope (δ 15 N) analyses to assess the origin of N sources. Intense green macroalgal blooms occurred during the first summer after flooding and diminished in the 2 following years as a result of rapid water exchange. Low δ 15 N in macroalgae in the first year (mean ± SE, 4.2 ± 0.3) increased significantly in the next year (8.0 ± 0.1). A laboratory experiment tested the δ 15 N response of opportunistic green macroalgae (Ulva spp.) exposed to organic manure and synthetic inorganic fertilizers. Higher δ 15 N (11.1 ± 0.1) characterized manure-treated algae compared to fertilizer-treated algae (2.7 ± 0.2). Based on these field and laboratory results, we accept both hypotheses and conclude that the major N source supporting macroalgal growth in 2014 was derived from synthetic fertilizers; however, rapid tidal flushing during the following years resulted in nutrient limitation and lower macroalgal growth.