That meant there was scant evidence to show when and why changes happened, with the lakes' natural condition largely remaining unknown, limiting the ability to set realistic restoration aspirations and meet ecosystem health limits.
But Dr Vandergoes and his team could still draw on lake sediments ("geological whakapapa"), which stacked year upon year, preserving indicators of lake life, water quality and the 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," she said.
The team would travel from lake to lake, using small boats to collect up to four sediment samples from each site.
Those samples would be analysed using methods ranging from DNA and radio-carbon dating to tests on pollen and charcoal fragments that could pinpoint 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," she said.
"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," Dr Vandergoes added.
"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," he said.
The findings would be used to predict future changes, and inform protection and restoration efforts, on a national scale.
Long-term monitoring data showed levels of total nitrogen, total phosphorus, algal indicator chlorophyll-a and visual clarity had generally improving over the period 2004 to 2013, but trends had been worsening for bottom-water dissolved oxygen and nitrate-nitrogen.