Due to its catchment size and its significant level of agricultural pollution, the Nemunas river basin has been identified as an agricultural hot spot in the Baltic Sea basin. On average, the total annual inorganic nitrogen runoff into the river is 26.9 × 106 kg, which corresponds to a load of 275 kg km−2 yr−1. A submerged floodplain, covering 605 km2 of the River Nemunas lowland, maintains the natural retention threshold for pollutants in the water of the main canal and the outfall at Curonian Lagoon, as well as improving farming conditions in the inundated meadows of the valley. It also increases the sedimentation and nitrogen retention capacities of the Nemunas catchment. It has been estimated that about 40% of the fine suspended sediments can be retained and deposited in the flooded meadows of the delta. Controlled inundation of the floodplains in the Nemunas delta may reduce its runoff nitrogen load by 21 kg km−2 per flood event. As a result, nitrogen concentration decreases by approximately 8–10%, causing a self-purification process in the flooded area. Nitrogen retention is dependent upon the velocities of the flood current and has mostly been observed in zones of stagnating water.

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