The river runs into Kaipara Harbour, which is an important breeding ground for snapper.
Environment Court Judge Brian Dwyer said a wetland on which earthworks were done was indigenous in nature and warranted protection provided in the Regional Plan.
He said the extent or significance of effects from unauthorised activities could not be accurately assessed as works have been ongoing for 18 months before the Northland Regional Council became aware.
Judge Dwyer classed their offending as moderately serious, rather than minor. He said had it involved more pristine wetlands or more identifiable, rather than potential, effects on the water systems, the offending would have been regarded as serious.
Although there was no evidence Mr Webster and his company were aware their actions breached the Regional Plan, enquiries should have been made with relevant authorities.
Failure to do so must fall in a scale somewhere between extreme naivety and wilful blindness, Judge Dwyer said.
"Mr Webster's inability to advance any explanation for his failure to make enquiry (I record that he was given the opportunity to do so) falls towards the latter or higher end of that scale.
"At best there was a complete lack of care on his part and at worst downright recklessness."
He ordered both to pay $7650 on each of the seven charges, or a total of $53,550. The Northland Regional Council will receive 90 per cent of the fine to cover costs associated with investigation and prosecution.