However, a significant step required to finish the project and generate the energy was the flooding of a 41-square-km of the dam reservoir. Soil and plants naturally contain mercury and the flooding can cause them to release carbon that triggers a process called methylation, resulting in the formation of a toxic substance -- methylmercury [1].

Given the methylmercury issue, the Nunatsiavut government, representing Inuit Nation in Labrador, started a "Make Muskrat Right" campaign. It was stated how Nalcor's mega-project wasn't properly managing the risk of contaminating the Churchill River with methylmercury, which, in turn, could flow downstream to Lake Melville, where many Inuit people live [2].  While methylmercury accumulates in Inuit territory, Inuit communities will see no benefits from Muskrat Falls, the campaign furthermore argued.  Despite high levels of energy insecurity along the Labrador Inuit coast, all of the power is being exported out of the region, the Inuit protesters living off the site continued [3].

The Nunatsiavut Government said how the reservoir flooding now underway leaves Inuit Peoples vulnerable to physical and cultural harm associated with anticipated increases in methylmercury contamination traditional foods, such as fish [3]. 

People started to openly protest against the flooding step required as the company argued. Protests included a hunger strike by three Inuit from Labrador, who refused to eat until a political resolution was reached [2]. Some protestors were arrested during the occupation of the Muskart Falls [4] [3]. Furthermore, Nalcor offered three Indigenous governments in Labrador one-third of the $30 million in compensation. Innu Nation and NunatuKavut Community Council accepted $10 million each – but Nunatsiavut representing the Inuit Nation refused the money [3]. 

The Nunatsiavut government later launched a study with Harvard University scientists, "which concluded that methylmercury levels indeed could rise as much as 380 percent in Lake Melville if the reservoir was not cleared of trees, plants and soils, before the flooding. The researchers said that increase could be drastically reduced, to 13 percent, if the reservoir was fully cleared [1] [2]".

Inuit protesters and Nunatsiavut's natural resources minister have publicly said they don't oppose the project itself, but would like that the project is done "right" — and that is to minimize the risk of methylmercury contamination [2].

"Nalcor Energy predicted no significant downstream impacts of the dam. Credible and independent new evidence shows that their predictions were wrong." [3] At the same time, Nalcor Energy has also commissioned studies and says that although methylmercury levels could increase in the reservoir itself and "immediately downstream" in the Churchill River, it would likely be diluted before reaching Lake Melville [2].

The local people continued to protest and stated:  “With reservoir impoundment underway, the time bomb is ticking on the future of those who depend on the Churchill River and Lake Melville for sustenance, and on the health, culture, and way of life of many Labrador Inuit" [2]. Many non-Indigenous people in local communities, including Happy Valley-Goose Bay, were supporting the Labrador Inuit in their protest [2].

A meeting between both sides was set, and after an 11-hour of negotiations, the Labrador government promised it would seek further independent assessments of the project and create a special committee to look at ways to reduce possible methylmercury contamination. Still, the Labrador government made no promises about fully clearing vegetation and soil from the Muskrat Falls reservoir [2].

Then, Nunatsiavut Leader called on the protesters to go home and for the hunger strikers to stop [2]. However, protesters who had occupied the Muskrat Falls workers quarters on Oct 22nd, 2016 walked out on Oct 26th, 2016 still having concerns over the flooding of the reservoir [5].

Two years after the dam project started (2018), protesters said the provincial government and Nalcor overlooked the dam's construction, and have not addressed the dam's impact on their culture [4]. They are still worried that the land they live on, and the wild food they rely on, will be damaged by the hydro-electric development's flooding and resulting in the rise of the methylmercury levels [4].

UPDATE OCT2020: "The Innu Nation of Labrador announced Oct. 6 that it is seeking $4 billion in damages from Hydro-Quebec over its mega-dam on the Upper Churchill River. The suit, filed in the Supreme Court of Newfoundland & Labrador, seeks compensation for the theft of ancestral Innu land in 1967." [6]

On November 20, 2017, the Government of Newfoundland and Labrador established the Commission of Inquiry Respecting the Muskrat Falls Project to investigate project mismanagement, delays, cost overages, and issues with Indigenous consultation. The project was initially estimated to cost (Canadian dollars) $6.2 billion, it has now run over $12.7 billion in cost and is still not fully operational as of June 2020.

The Muskrat Falls Inquiry found that Nalcor acted irresponsibly in many different aspects of this project (financially, management-wise, environmentally, and with regards to Indigenous consultation and communication). A summary and list of applicable quotes from the summary can be found here (https://docs.google.com/document/d/1aXjNDNafUQvYYsOmhRdDjFUERlvRNnGxlPck0hKf2NM/edit?usp=sharing).

The construction of the Muskrat Falls project involved the flooding of lands to create reservoirs that disturb trees and soils. Natural processes transform those materials into methane, a powerful greenhouse gas. Life-cycle emissions of some large scale hydropower facilities can be over 0.5 pounds of carbon dioxide per kilowatt-hour. Natural gas burning for comparison has life cycle emissions averaging between 0.6 and 2 pounds of carbon dioxide per kilowatt-hour. According to Brazil’s National Institute for Space Research, the world’s large dams are responsible for 23% of all methane emissions due to human activity.