The EPA's 2014-15 annual report issued last week also warned that the lack of "solid understanding" about the impacts of resources sector activity on critical habitats could mean resources projects are planned and even approved in inappropriate locations or times.

The EPA said in its report that assessing the potential impacts and risks associated with activities like dredging, increased vessel traffic and noise and percussion generated by construction activities was "hampered by incomplete knowledge".

"For example, the population sizes, distribution and habitat usage requirements of important marine fauna such as dugong and turtles are not well understood and for some types - such as coastal dolphins - there are very large gaps in understanding," the EPA's report said.

Further, the EPA warned that "in the absence of a solid understanding of key critical habitats and how natural environments behave and fluctuate naturally over time, it is possible that projects or activities could be planned and approved in inappropriate locations or times, or conversely ‘impacts' wrongly attributed to an activity when they may be ‘natural'".

EPA chair Paul Vogel admitted to Energy News that there was a "lack of understanding" of environments that are impacted by the resources sector.

For example, he said there was "some uncertainty" around the impacts of dredging, which is why the agency produced the WA Marine Science Institute's Dredging note to reduce those uncertainties in understanding the impacts of turbidity on coral.

This, he said, was linked into increasing the level of understanding about the impacts.

He said there was an urgent need to improve the science and understanding about how those systems will respond to impacts, otherwise he could foresee two scenarios playing out - and neither of them would be good for industry or government.

"If we don't have that level of certainty - and it will never be 100% - we will end up with circumstances where the uncertainty and risks are so high that the [EPA's] recommendation is ‘no'," he said.

The other alternative effect of such uncertainty, he said, was that "it becomes so high that you end up with such stringent conditions that they are incredibly complex and costly to implement, and difficult to enforce".

"So we make sure companies understand the environment they're impacting, predict the impacts on those values, and also have reference sites, which is the key point made in the annual report."

The key thing to remember, he said, was that the environment was dynamic.

"It changes constantly, and if you don't have good reference sites and good information about them, then you may attribute change that might be natural to the impacts of a project," he said.

"We had some very real examples of that with the Wheatstone project, where there was a natural coral bleaching event and they looked at the reference site and said the reference sites were nearly all dead, therefore we need to re-adjust how this project and all the conditions work.

"But if we didn't have that information you could easily potentially attribute the coral bleaching to the impacts of dredging, and that clearly was not the case. So you need the reference sites and increasing science and knowledge to inform impact assessments and that reduces the predictive uncertainty over time.

"But we also need to understand that the environment is a very dynamic place and that there can sometimes be massive natural variation, in that case around a changing climate and changing sea temperatures.

"We need to be taking those things into account in making judgements and advising government."