The judge said sufficient information was not supplied to the farm manager in that he was neither given a copy of the resource consent nor the abatement notice.
Flood mentors young farmers and in 2008 he was declared the Rabobank Executive Development Programme Management Project winner.
Judge Whiting said it was important farmers realised the drainage systems on their properties were not just the end of the problem.
He said the feed pads were badly constructed and were adjacent to drains and tributaries, including one that at least sloped towards a drain.
The court accepted Flood's actions were not deliberate. However, Judge Whiting said a deterrent signal needed to be sent out to the dairy industry in Northland that it was time farm owners scrubbed up and accepted responsibility for dairy discharges.
"That such a signal is necessary is reflected in the poor non-compliance statistics of dairy farms in the Northland region, as put before me by the regional council," Judge Whiting said.
Flood initially said he had no means to pay a fine beyond the $6000 he had in savings but the court made an order that he file a declaration after learning he had an interest in corporate entities that owned seven dairy farms.
A forensic accountant hired by the regional council reported that the Flood Group had the ability to meet its debts and its assets were greater than liabilities.
Apart from the $53,000 in total fines, Flood was ordered to pay $4945 in forensic accounting fees and about $400 in court costs.
The fines and costs will be paid over nine months.