There was evidence that cows had been fed in the paddock as there were makeshift feed troughs there.
Some of the paddock was churned up and there was no grass - the product of animals being kept there for a reasonable period of time.
There were some mounds of soil and effluent combined and there was a large area of ponded water.
Inspectors also found a number of holes had been drilled around the edge of the water and there was water flowing into them.
Mr Pilditch said the concern for the regional council was that once there was a pond of water it could become too much for the soil and there was a risk of the effluent getting into the ground water and then into the waterways.
Mr Pilditch said Crafar was spoken to and he had said he had used one of the paddocks as a "sacrifice paddock" in bad weather and admitted drilling the holes.
A sacrifice paddock is a grassed area which has been allowed to be grazed completely, to be cultivated and resown later.
Crafar is representing himself but has a Mackenze Friend or court assistant.
In his defence, Crafar gave a brief opening statement and told the jury he was innocent and had not breached any section of the Resource Management Act.
"I've been living on or by the farm all my life. I've been in farming my entire life."
Crafar said there was no way the "pond or puddle" could have ended up in the ground water.
He said the ground water was 80m deep and there was no running water within at least 8km of the paddock.
He said in accordance with Environment Waikato rules he had wanted to work the land and sew it into a crop.
Crafar said the paddock was an ex-crop paddock and had been used to grow turnips.
He said he had used a sucker tank to suck the water away.
Judge Chris McGuire is presiding over the trial which is expected to finish tomorrow.