John Carruthers dug out the stream on his farm in 2010 and then allowed cattle to roam in the area, delaying the recovery of fish and plant life.
He unsuccessfully fought the prosecution brought by the Otago Regional Council in April, arguing he had the right to clear out the on his farm.
In the Dunedin District Court on Friday, Judge Newhook found the offending led to effects that were no more than minor on the creek the stream flowed into, and the Taieri River further down.
Judge Newhook said the farmer had a prior good character, but needed to be sent a message that he did not have the right to do stream works without a resource consent.
He fined Carruthers $5400 and court costs of $1663.