Causes of eutrophication. The main causes of eutrophication are. 1  natural run-off of nutrients from the soil and the weathering of rocks. 2  run-off of inorganic fertiliser (containing nitrates and phosphates).3  run-off of manure from farms (containing nitrates, phosphates and ammonia).he main causes of eutrophication are. 1  natural run-off of nutrients from the soil and the weathering of rocks. 2  run-off of inorganic fertiliser (containing nitrates and phosphates).
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