George Phelan, appeared in court charged with carrying out unauthorised activity in an area under special conservation.
The case was brought to court after Conservation rangers spotted diggers on the land of the accused in the river valley carrying out work.
The farmer was then advised by a conservation ranger to cease digging operations on the conserved site as he did not have consent.
When the conservation ranger and two colleagues returned to inspect the site at a later date the found more evidence of work carried out by the diggers on the land.
They found that a kilometre-long embankment had been completed on the river valley.
The court heard how this disturbance of river sediments can affect river populations and also noted that the destruction of river bank vegetation is a risk to otter populations.
The court also heard how the accused, Mr. Phelan, felt he had no other alternative after the floods of 2014 left huis land under up to 12 feet of water.
The farmer said he was only protecting his livelihood and says he would seek permission for such works in the future.
The case was taken by the Department of Arts, Culture, and The Gaelteacht against Mr. Phelan.
Mr. Phelan was fined €150 for the offence, and was given a deadline of 6-months to pay it.