Watsiana Pty Ltd admitted that the pollution could have made or could reasonably be expected to  have made the waters poisonous, harmful or potentially harmful to animals, wildlife, fish or other aquatic life or similarly damage plants or other vegetation.

Described in Melbourne Magistrates Court on Wednesday as a small family company run in the Bendigo area for more than 30 years, with brothers Mark and Grant Austin directors, Watsiana was also ordered to pay $11,223 in costs.

Magistrate Phillip Goldberg did not convict the company, which has no prior convictions, and took into account its previous good character, early guilty pleas and the delay in finalising the case.

Mr Goldberg said any fine - the company faced a maximum fine of about $293,000 - must demonstrate to any corporation it should not implement works with the potential to cause pollution.

Kevin Armstrong, prosecuting for the Environment Protection Authority, said the authority received a pollution report on September 23, 2011, that "turbid" waters were being pumped from a sediment basin on the site into Back Creek.

Mr Armstrong said the Back Creek occasionally flowed, depending on rainfall, and that a planning scheme for the premises provided an environment overlay for the area that meant any works had to be done to limit disturbance and potential impacts to it.

A week later, the EPA issued a notice to Watsiana to ensure that no sediment was deposited beyond the boundary of the premises and that sediment controls be installed.

Following a second report of turbid waters being put into Back Creek from the premises on November 11, an EPA officer saw sediment laden water being pumped from an onsite sediment dam and discharging into the creek.

Mr Armstrong this was in contravention of two requirements of the notice while the officer saw a "sediment control contraption" that had been constructed with turbid waters exiting from a large black pipe with holes that allowed flows offsite.

Samples taken that day included one that showed the "turgidity" of the water discharging into Back Creek at 200 times that acceptable according to an EPA guidance document.

Defence barrister Jason Gullaci noted that the offences did not involve deliberate acts, the  spillage of petrol, chemicals or oil or any actual damage or harm to wildlife or vegetation.

Mr Gullaci said Grant Austin had decided on the second occasion to pump water out without "appropriate supervision" and that inappropriate measures were not in place on November 11.

He also submitted that EPA had reattended the site a number of times after the first incident and that the Austins were never told their improvement measures were unsatisfactory, to which Mr Armstrong responded there had been advice given but the measures were not "checked off".

In his sentencing remarks, Mr Goldberg said it was "obvious" that the work done after September 23 was not appropriate or the materials used were applied appropriately, but agreed that "some steps were taken" to meet the company's obligations to prevent pollution.

He regarded the offending as in the middle range and noted that Watsiana was now a smaller business and no longer did earth work.