This discharge and the contingency pond overflow entered the same channel and flowed into the same farm drain, then into the Waitahanui Stream.
The stream is a habitat and migratory pathway of indigenous fish species, and ultimately flows into the sea about 10km from the farm.
The regional council's lawyer Adam Hopkinson said these unlawful discharges had resulted in "immeasurable" changes to the stream and ultimately an important regional habitat.
Mr Hopkinson urged Judge Jeff Smith to impose a fine of up to $60,000, saying this prosecution was "symptomatic" of the same underlying compliance issues that had been occurring on the farm for some time, with an abatement and an infringement notice having been issued in the past.
He said the defendant had taken a "minimalistic and reactive approach" to the problem which could have been avoided with better farm management practices.
Bayfield Farms lawyer Peter Hardie argued the fine sought was excessive, pointing out that his client conceded he relied too heavily on his farm manager, but he had since taken remedial steps to ensure the problem did not recur.
Judge Smith said while the underpass discharge had been an "unexpected and untoward event" both discharges did flow into the stream, and therefore this was serious offending.
The judge said a fine of $35,000 was appropriate and fair after allowing the company discounts for guilty pleas, remorse, and its clear intentions to avoid further offending.