Others ranked "poor" included Lake Tutira in Hawke's Bay, Lake Rotorangi in Taranaki, and Lake Hayes in Central Otago. Photo: Craig Baxter

Scientists have begun a sprawling health-check of hundreds of New Zealand lakes, at a time where monitoring data shows more North Island spots are graded bad than good.

In a five-year, $12m project, led by GNS Science and the Cawthron Institute, researchers will try to find out how 380 lakes around the country have changed over the past 1000 years.

Dubbed Lakes 380, and supported by the Government's Endeavour Fund, the ambitious study will offer a snapshot of around 10 per cent of New Zealand's lakes larger than 1ha.

"Currently there is limited data on the health of only five per cent of these lakes, and this only monitors water quality over the past decade," said study co-leader Dr Marcus Vandergoes, a GNS paleoclimate scientist.

That meant there was scant evidence to show when and why changes happened, with the natural condition of lakes remaining largely unknown.

"This limits our ability to set realistic restoration aspirations and meet ecosystem health limits."

The data collected deemed Lake Waihola's water quality as "poor". Photo by Gregor Richardson.

But Vandergoes and his team could still draw on lake sediments - or what he called "geological whakapapa" - which were stacked year upon year, preserving indicators of lake life, water quality and the surrounding catchment.

Fellow programme leader and Cawthron scientist Dr Susie Wood said the sediments effectively provided the equivalent of centuries of monitoring.

"These natural archives will provide the knowledge we need to understand the drivers of environmental change and restore the ecological vitality of our lakes."

The team will travel from lake to lake, using small boats to collect up to four sediment samples from each site.

The gathered samples would be analysed using methods ranging from DNA and radio-carbon dating to tests on pollen and charcoal fragments that could pin-point the time when surrounding land and bush was cleared.

Cawthron social scientist Dr Charlotte Sunde said the project would also work in partnership with iwi and hapu.

"We will be guided by matauranga Maori [knowledge] and oral histories to enrich and inform our joint aspirations for enhancing these taonga, our lakes."

"The study will provide knowledge on how divergent lake health is from its natural pre-human condition and highlight what variables have caused this change," Vandergoes said.

"For example, it might show that the presence of native aquatic species like plants and fish has varied, or the effect of introduced species on native biodiversity."

While some lakes had changed little, others had undergone "significant" transformation.

"As far as we know, this study will be the first national-scale quantification of human impact on lake health globally, providing a unique opportunity to test explore how lake health has changed regionally and nationally."

The findings will be used to predict future changes and inform protection and restoration efforts, on a national scale.

How healthy are our lakes?

The study comes as more than 50 lakes monitored through the jointly-run Land Air Water Aotearoa (LAWA) website are graded either very poor or poor for water quality.

Among those graded worst were Lake Rototuna in Northland, Lake Waikopiro in Hawke's Bay, Lake Horowhenua, Lake Wairarapa, and Lake Ellesmere and Lake Rotorua in Canterbury.

Others ranked "poor" included Lake Tutira in Hawke's Bay, Lake Rotorangi in Taranaki, and Lake Hayes in Central Otago.

The best-rated lakes included Lake Waikaremoana, Lake Ohau, Lake Tekapo, Lake Manapouri and Lake Te Anau.

New Zealand's largest, Lake Taupo - recently hit by an algal bloom scare - was graded "good", as were Lake Tarawera, Lake Okataina, Lake Dunstan and Lake Wanaka.

Lakes rated good or very good tended to be clear, with low concentrations of nutrients and algae, while those rated poor or very poor were typically turbid, with high concentrations of nutrients that fuelled frequent algal blooms.

These lakes were rarely suitable for swimming and, in some cases, couldn't even support native freshwater species.

The gradings were based on the Trophic Level Index (TLI), which combined four water quality indicators to signify a lake's life-supporting capacity.

Of 65 lake sites monitored between 2009 and 2013, 24 sites had median TLI scores of very good or good, 17 monitored sites had moderate scores, and 24 monitored sites had poor or very poor scores.

Over the same period, 12 sites had phosphorus levels too high to meet national

bottom lines for ecosystem health, 11 had too much nitrogen, and 11 had unacceptably high levels of algae biomass.

This meant these lake sites could have ecological communities at high risk from nutrients causing algal blooms, or from not enough oxygen.

Long-term monitoring data showed levels of total nitrogen, total phosphorus, algal indicator chlorophyll-a and visual clarity were generally improving at lakes over the 2004 to 2013 period, but trends had been worsening for bottom-water dissolved oxygen and nitrate-nitrogen.

Lake water quality at a glance

NORTH ISLAND

VERY POOR:

Lake Rototuna, Lake Kuwakatai, Lake Runanga, Lake Waikopiro, Lake Dudding, Lake Horowhenua, Lake Wiritoa, Lake Wairarapa, Lake Waitawa, Lake Waikare

POOR:

Lake Carrot, Lake Heather, Lake Kahuparere, Lake Ngakapua North, Lake Ngakapua South, Lake Ngatu, Lake Omapere, Lake Rotokawau (Aupouri), Lake Roto-otuauru/Swan, Lake Waiparera, Lake Waiporohita, Lake Hakanoa, Lake Maratoto, Lake Serpentine South, Lake Waahi, Lake Whangape, Lake Pupuke, Lake Tomarata, Lake Wainamu, Lake Rotomanuka, Lake Okaro, Lake Rotoehu, Lake Rotorua, Lake Opouahi, Lake Tutira, Lake Rotorangi

AVERAGE:

Lake Humuhumu, Lake Kanono, Lake Karaka, Lake Mokeno, Lake Morehurehu, Lake Rotokawau (Pouto), Lake Rotoroa, Lake Waihopo, Lake Wainui, Lake Waipara, Lake Ototoa, Harihari, Lake Okareka, Lake Rerewhakaaitu, Lake Rotoiti, Lake Rotomahana, Kaweka Lakes

GOOD:

Lake Kai Iwi, Lake Te Kahika, Lake Taupo, Lake Okataina, Lake Rotoma, Lake Tarawera, Lake Tikitapu, Lake Waikareiti

VERY GOOD:

Lake Taharoa, Lake Waikaremoana

SOUTH ISLAND

VERY POOR: Te Waihora/Lake Ellesmere, Te Wairewa/Lake Forsyth, Wainono Lagoon, Lake Johnson

POOR: Coopers Lagoon/Muriwai, Lake Emma, Lake Georgina, Lake Hayes, Lake Tuakitoto, Lake Waihola, Lake George, Lake Vincent, The Reservoir (Southland)

AVERAGE: Lake Haupiri, Lake Alexandrina, Lake Camp, Lake Clearwater, Lake Emily, Lake Grasmere, Lake Ida, Lake Lyndon, Lake Middleton, Lake Pearson, Maori Lake (back), Lake Onslow

GOOD: Lake Brunner, Lake Hawdon, Lake Heron, Lake Sarah, Lake Selfe, Lake Taylor, Loch Katrine, Maori Lake (front), Lake Dunstan, Lake Wanaka

VERY GOOD: Lake Aviemore, Lake Benmore, Lake Coleridge, Lake Ohau, Lake Sumner, Lake Tekapo, Lake Hawea, Lake Wakatipu, Lake Manapouri, Lake Te Anau

• Source: LAWA. Not all lakes are included