The Natural Resources Access Regulator (NRAR) brought the case in the LEC for offences which took place between 2016 and 2020 on a property at Tea Gardens.

The offences impacted Station Creek and some of its tributaries joining Bundabah Creek, which is part of the North Arm Cove Sanctuary Zone of the marine park.

The company was found guilty by the court of four offences under the Water Management Act. This included building two unauthorised dams and clearing vegetation, which also contained an endangered ecological community.

NRAR chief regulatory officer Grant Barnes said protecting the health of watercourses and waterfront land was a key focus of the agency and was important to the community and environment.

"What landholders do in and around waterways can have serious negative environmental consequences and that's why landholders must apply for approval for any works before they start, and follow any conditions of approval," Mr Barnes said in a statement on Thursday.

"Approvals usually contain conditions to minimise negative impacts, and NRAR is committed to holding landholders to account if they don't follow the rules, and to prosecuting the most serious breaches."

Justice John Robson handed down significant sentences for each of the four offences, noting that by not applying for approvals the company had "sought to avoid the regulatory scheme and its beneficial protection of water sources and waterfront land".

Justice Robson also said the activities had "significantly undermined the objectives of the Water Management Act".

For the removal of vegetation and endangered ecological community, the company was fined $64,600.

For clearing vegetation and depositing material within 40 metres of a water course, it was fined another $57,000.

Justice Robson fined the company a further $64,600 for constructing an unauthorised dam on a watercourse. The dam has now been removed.

The company was fined an additional $64,600 for building an illegal dam on another stream at the same location. The landholder was ordered to reform a spillway to replicate a natural channel and slow water flow and implement a vegetation management plan within three months of it being approved by NRAR.

The court further ordered that the stream bank vegetation corridor around this dam be widened by the landholder.

The company has been ordered to pay legal costs of NRAR in an amount yet to be determined, and to publicise the matter in digital and print publications across the region.

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