Dr Smith visited the lagoon today where he talked to Environment Southland and locals about issues facing the internationally-recognised site, which is part of the Awarua wetlands southeast of Invercargill.
"Regular monitoring is showing that water quality in the lagoon has declined over the past 10 years as a result of increasing sediment and nutrients," he said.
"The catchment has high ecological diversity so it is vital all stakeholders work together on agreed solutions to stop the lagoon degrading further."
Dr Smith said the Government had faith in the collaborative approach to resolving challenging environmental issues.
"There is a huge challenge for Environment Southland in reversing the pollution that is putting the Waituna Lagoon at risk," he said.
"The Government is willing and able to provide support for the cleanup."
The Green Party earlier today called on the Government to restrict cattle numbers in the lagoon's catchment to save it from dairying pollution.
"The regional council has failed in the past to put in place rules to limit the number of cows and now central government needs to step up to the plate to help clean up the mess," he said.
"It has an international obligation to protect the lagoon and has ample powers to intervene."
Dr Norman said Dr Smith should make it clear to the regional council and the dairy industry that central government would reduce stock numbers if they didn't sort it out themselves.
A recent Environment Southland monitoring report said the lagoon was under threat from high levels of nitrogen and phosphorous as a result of dairy farm runoff.
Southland Conservation Board said last week the next heavy rain could have dire consequences.
