A physical‐biogeochemical model is used to simulate the evolution of the δ15N signal during the last glacial‐interglacial transition in sedimentary cores offshore from the Mauritanian upwelling. The biological model is a classical nitrogen‐based trophic chain model, which also computes the nitrogen isotope fractionation. The 2D physical primitive equation model simulates the coastal upwelling circulation and is applied for different sea level scenarios. The effect of the sea level rise, inducing the shelf immersion, seems to be a main factor explaining the organic nitrogen flux and isotopic signal variations along the last deglaciation. This effect is modulated by an upwelling seasonality that may have been much longer at the Last Glacial Maximum, around 10–11 months instead of 4–5 months at present. Between 15 and 5.5 kyr ago, 60% of the sedimentary δ15N variations could be explained by this local shelf immersion effect. This reconstruction also reproduces the strong isotopic fall occurring between 5.5 kyr and the present.