Enter the Waikato Regional Council (WRC) which, along with the Lake Taupo Protection Trust, iwi, Taupo District Council and central government worked out how to address the problem. A nitrogen trading system was developed, making available an $81 million fund to incentivise land use change and buy nitrogen credits and land from land owners.
It works by capping land owners at their highest nitrogen usage from their most intensive year between 2001 and 2005 under a system known as 'Variation 5'. If they want to increase this level, for example by intensifying a dairy farm, they have to buy credits.
Credits are created by landowners from land use changes - retiring unproductive areas of pasture and turning them into forest or downsizing operations. This leads to smarter farming decisions - rationalisation of land and better choices about where to farm.
The long-term goal is the protection of water quality, keeping it at 2001 levels while reducing the amount of nitrogen in the lake by 20%. Dairy farms make up only 18% of the catchment but add 90% of the nitrogen load to the lake. Urban nitrogen has also been addressed by upgrading sewage systems.
According to Natasha Hayward, from the WRC, the water in Lake Taupo takes around 50 years to filter through the soil and reappear as lake water. "We have to remember it is a long-term project. The effects of what we're doing now won't be visible until around 2080".
Variation 5 has been a success, despite initial reluctance. New dairy and dry stock farming, above a certain stocking level, will now require consents, in contrast to the rest of the country where farming is a permitted activity without any conditions on agricultural runoff.
New Zealand is an agricultural nation. Forty per cent of land is devoted to agriculture, with a total of 1.5 million hectares in dairy farming. Agriculture contributes five per cent to our GDP, with the dairy industry alone accounting for 2.8% and $10.4 billion of export earnings.
Over the last half century, agricultural practices have emphasised external inputs - nitrogen and phosphate-rich fertilisers, pesticides and feedstuffs like palm kernel which come at the expense of endangered species and rainforests in Borneo and Indonesia.
Urea fertiliser alone increased 162% between 1996 and 2002. This puts pressure on the environment, jeopardising soil and water resources.
Farming continues to intensify, and why wouldn't it? Demand for agricultural products - particularly dairy - continues to increase as Asian markets blossom. Between 1994 and 2002 the number of dairy cows increased by over a third, while land for dairy farming increased only 12%. The number of cows shot up by two million between 1992 and 2011, with the national dairy herd now comprising more than 4.5 million cows.
As farming intensifies, fertiliser use and stock numbers rise. Treeless fields cause soil erosion when it rains which washes, unhindered, into waterways. Nitrogen and phosphates from fertilisers as well as nitrogen-rich cow urine are the biggest agricultural problems.
"To get an idea of the scale, the urine produced from the national dairy herd is equivalent to that from 80 million people, but without the sewage treatment," says Green Party water spokesperson, Eugenie Sage.
In major farming regions, water quality continues to decline.
The Resource Management Act (RMA) only addresses pollution that comes from a particular spot - 'point-source pollution'. It fails, however, to address 'non-point pollution' such as agricultural run-off. Non-point pollution has been called "the most serious freshwater management challenge in New Zealand today" by the Ministry for the Environment.
Other councils have come up with good ideas to support rural landowners to address this problem, like Environment Waikato's Clean Streams Fund. This contestable fund provided a pool for fencing, to keep stock from letting rip in our rivers, as well as supporting planting of waterways which stabilises bankside areas, absorbs some of the agricultural runoff and reduces sediment loads to waterways.
Following a period of targeted funding to land owners in Bay of Plenty, the BoP Regional Council introduced 'Rule 8', which punishes farmers who let their livestock meander the streams that surround the Rotorua lakes. The Council still supports streamside protection through the Riparian Management Programme.
The mix of 'carrot' (specific funding support) and 'stick' (regulation) has meant that landowners have been financially supported to make good decisions about riparian areas.
The city:
Waterways that flow from mountains to the sea pass through another noxious environment - the city. The sullied creeks trickling through urban areas are rarely considered to be 'life-supporting', but fish and insects are still there, struggling to survive.
Sewage systems began with 'night men' gathering the 'night soil' from houses, but moved to piped sewerage systems imported from the Motherland, based on the Victorian idea of water being a 'conduit for waste'. Thus, our cities inherited a legacy of pipes - a system that is expensive to change and maintain.
Toxic runoff from cars is just one of the impacts of plastering our cities in concrete. Around 70% of the nasties in storm water runoff, from lead to zinc to copper, are caused either directly or indirectly by our love affair with cars.
More cars, says Dr Sam Trowsdale from the University of Auckland's School of the Environment, means more roads.
"What we really need to do is focus on source control - we need to eliminate the source of contaminants and the source of the problems. We need to reconfigure our city and redevelop so that we are less reliant on cars. This will reduce the amount of impervious surfaces and the amount of big, smooth roads."
When it rains, water rushes over 'hydraulically efficient' surfaces from rooftops to roads, and is funneled down drains, collecting litter, driveway-car-wash detergent and pollutants.
In older parts of Auckland city, combined systems mix this so-called 'storm water' with 'waste water' - water from kitchens, laundries and bathrooms. This is piped to the wastewater treatment plants where water is 'treated' and discharged into the sea.
Combined sewage systems, however, are not designed to deal with high rainfall. Increases in storm water can cause them to overflow, spilling sewage into rivers or the sea. Beaches like Cox's Bay, Meola Reef, Kawakawa Bay, Weymouth Beach and Little Oneroa Lagoon have permanent health warnings because of the high levels of E.coli - a bacteria indicating the presence of sewage.
Only a fraction of storm water receives any kind of 'treatment' before being discharged. Waterways are increasingly contaminated by zinc from tyres (found on our roads in tiny particles of rubber), from galvanised iron roofs, and from paint particles dissolved into rain water.
Copper from vehicle brake linings, soil, cement, and shiny spouting runs across our impervious cities, down the nearest drain and into the water.
Our human impacts may be invisible to the naked eye, but they are adding up. In 2004, Auckland Regional Council reported that zinc concentrations were high enough in urban streams to kill some creatures and exert a major influence on estuary-dwelling creatures. This water gets absorbed by shellfish, which we consume. They are also consumed by the snapper that we fish from the harbour every day. Everything is linked.
Worse still many pollutants bio-accumulate up the food chain meaning that the higher-up you are the higher the exposure levels.
In many sites levels of copper, lead and polycyclic aromatic hydrocarbons (PAH - resulting from incomplete combustion of petrol as you start your car) also exceed the 'amber' levels (compared to green - 'good' and red - 'bad'). Whilst lead concentrations are decreasing because it has been removed from petrol, zinc and copper are on the up - especially as land use changes from rural to urban.
Should we be aiming for 'tipping points'?
There is a better way for us to work with our environment, says Dr Kepa Morgan, senior lecturer in civil and environmental engineering at University of Auckland and of Ngati Pikiao, Te Awara, Ngati Kahungungu and Ngai Tahu descent.
His concept, the Mauri Model, aims to preserve the mauri of waterways, or the "binding force between the physical and the non-physical attributes of water." It's simple, he says.
Either we're enhancing the mauri - making it better, something we ideally should be aiming for when we problem solve, or we're not.
"When you put rubbish into water, you diminish the mauri and eventually you get that 'tipping point', where the water no longer has the capacity to support life or to even regenerate its own mauri."
The strength of the mauri leads to different classifications of water. Many emphasise physical attributes, such as wai tai (salt water) or wai maori (fresh water) or metaphysical aspects. Water may have historical connections and knowledge associated with them. For example wai kino ('bad' water) may signify that the water is not fit for drinking or swimming. Other examples include wai tapu (sacred water), wai apu (swallowing waters - dangerous to cross in flood), wai ariki (chiefly waters - indicating the presence of hot springs or curative water).
Rainfall is considered wai tapu. Water from the sky is 'nga roimata o Ranginui', the teardrops of sky-father Ranginui. Rainfall is considered tapu until it has travelled over or through Papatuanuku, the earth-mother.
Many houses in Te Urewera do not have gutters on the roofs of the wharenui, to ensure that water falls directly onto Papatuanuku, says Morgan. The mixing of two water bodies with different mauri is against Maori protocol, and is based on common sense. In the Wai-8 claim Maori were against using water from the Waikato River as a coolant for the Glenbrook Steel Mill.
This is because the water was discharged into the Manukau Harbour, an area that the river does not naturally flow into. Water from the Waikato, which has a high naturally-occurring level of arsenic, would therefore have had a detrimental impact on the ecosystem of the harbour, states Morgan.
Morgan has taken his Mauri Model to many conferences, including the annual conference of Institute of Professional Engineers of New Zealand, where it was used to analyse wastewater systems in New Zealand. Unsurprisingly, this model showed that conventional systems were unsustainable. He says an ethic of kaitiakitanga, which describes the obligation and responsibility that comes with stewardship, would avoid diminishing the mauri in any way at all.
Morgan says that the sustainability movement and concepts such as environmental engineering are re-establishing the forgotten link between engineering and ecology.
Urban development acronyms like Low Impact Design, (LID), Sensitive Urban Design Systems (SUDS), Water Sensitive Urban Design (WSUD) and Water Sensitive Cities (WSC) are not only good artillery at a dinner party, but also inspiring us to move forward in a less destructive way.
All have the same ideas in mind - reminding people of the connection between humans and nature.
Dr Trowsdale says we are too focused on 'treating' our water rather than protecting it. "If we had to protect our water source we wouldn't be allowed to use products that polluted our water in the first place. With our drinking water we think we can just pollute it, because it's sent to a treatment plant."
Trowsdale asserts that a 'protect paradigm' would stop people pouring paint down our drains, and prohibit the disposal of industrial chemicals into sewerage system; a system which toxifies our sewage waste meaning it has to be landfilled rather than being reused as fertilisers.
Environmental education groups like Auckland's Wai Care are working with children and community groups, proving that our waterways are far from dead. Through riverside restoration projects, creatures like fish, small insects and eels benefit, while stronger communities are forged that respect and nurture the natural world.
Urban restoration projects like Waitakere's Project Twin Streams is revegetating 56 kilometres of stream banks in West Auckland with additions like rongoa gardens and pa harekeke (flax gardens) dotted amongst the native streamside plantings.
This is being done using a community development model that seeks to reconnect the community to the environment. With groups like these, and development paradigms that work with rather than against the environment, the future of our cities could be extremely livable and exciting.
Best Practice:
The inaugural Landcare Awards Dinner held last February showcased some incredible success stories around dairy farmers' stewardship of the water on their properties. Among them was Waikato dairy farmer Andrew Hayes, the recipient of a Landcare Award. His farm surrounds Lake Kaituna and forms a long border with Lake Komakorau.
It was clear to Andrew and his family that the lakes were dying and something big needed to be done. Restoration work began in 1999 and continues to this day, the result being that the lake is once again flourishing, with wildlife back on its waters in large numbers.
Our freshwater creatures
Two thirds of our freshwater fish, the 'canaries in the coal mine' of our waterways, are threatened or in decline. The koura - our only freshwater crayfish - and the kakahi - our freshwater mussel species - are also threatened. Around 90% of our freshwater fish are endemic, found only in New Zealand.
Long-finned eels are now at risk and declining. Their migratory life cycle means that when the time comes for large females to breed (at around 60 years old), weirs and dams block their passage, and pollution-riddled water means they might not make it to the deep trenches near Tonga where these mysterious fish reproduce.
These creatures are more endangered that the great spotted kiwi. Yet we still commercially harvest them. Non-commercial fishers are legally allowed to harvest six eels a day. The Ministry of Fisheries has introduced a maximum size limit of 4kg, however female eels grow larger than males, so are more likely to be fished.
Manaaki Tuna is an NGO formed to address the plight of our native Long-finned eel. Dr Mike Joy, member and ecologist at Massey University is highly vocal about their conservation.
"We have already lost about 75% of the population and we may get down to a level where there are not enough eels for the breed to take place. We are getting near that point now - this species could be virtually extinct overnight."