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The rural lobby organisation has launched its manifesto before this year's election, challenging political parties to take a sensible, practical and affordable approach to tackling issues of high importance to its members.
It supported a framework for catchment partnerships that co-ordinated community, council and scientific efforts.
''This could involve a range of taxpayer and region-wide rates-based funding to assist in the most cost-effective way to manage our regional waterways.
''This way we can target those hot spots that need immediate attention through applying science-based data, investing resources and funds more wisely, to understand and ultimately alleviate the worst affected areas,'' outgoing national president Dr William Rolleston said in a statement.
Catchment communities should have more say in how their waterways were managed as every catchment was unique in regard to its current state and how it should be managed in the future.
Much of the water quality debate was ''dominated by emotive slogans and assumptions based on skinny data, patchy scientific knowledge and highly speculative modelling''.
That led to problem definitions that did not accurately reflect the on-the-ground reality, the manifesto said.
''In the absence of a well-defined problem, there is no hope in developing cost-effective solutions that achieve the desired result - improved water quality,'' it said.
The Parliamentary Commissioner for the Environment highlighted most water quality challenges were local, not national, scale issues.
Efforts to maintain and improve water needed to be focused on priority catchments and not undermined by blunt, broad-bush national regulations and approaches.
Federated Farmers recommended greater focus and investment in biosecurity measures, in the wake of several high-profile biosecurity incursions in the past year.
If New Zealand suffered a foot-and-mouth disease outbreak, such as that which struck Europe in 2001, it was estimated the cost to the country would be more than $16billion.
The manifesto also asked for reform of the Resource Management Act where there was redress of economic priorities which underpinned rural economies and their social prosperity.