The Emajõgi river provides recreation opportunities for a large area of Estonia, and is the basis for a growing eco-tourism industry that mostly benefits local communities. Many eco-tourism companies have expressed their concerns over impacts on the river health and from increased logging.

In December 2017, the Estonian Fishermen's Community issued a very detailed statement, expressing opposition to the mill, due the high pollution it would cause to the Emajõgi river.

Forest management
The project's size is enormous not only by Estonian standards. The Est-For pulp mill will require 3,000,000 cubic meters of pine, spruce or birch wood each year - almost a third of total timber felled in the country each year. Timber will be mainly purchased from Estonia and partly from Latvia. The project developers state that the project would source timber from "existing wood flow", however forests in Estonia and Latvia are already overexploited, there is no commitment to use timber from credibly certified sources (FSC), and as such the project is expected to add to these problem. 

The way Estonia manages its forests is currently at a point where environmental organisations on one side and the state and private forest owners on the other disagree on what the maximum logging volume should be. EKO (Environmental Council of NGOs) claimes that "the state had no idea what the logging volume of the current year would eventually be, and had not made any efforts to effectively limit logging volumes. The state had no sufficient overview of the industry either. Surveys had already shown that the current disorganized approach negatively affected the forests and the habitats it provided to the local fauna."

A new large consumer of forest resources like the planned pulp mill would worsen the current situation. Before the next large investments, measures needed to be taken to guarantee a sustainable use of Estonia's forests, including the appropriate legal measures. A recent OECD report recommended: “Encourage sustainable forestry management, including by limiting the intensity of forest use, and disseminating knowledge on sustainable forestry practices among private forest owners.”

In 2016 a study on Fungal Ecology was published suggesting that intensive management of Estonian forests, especially spruce dominated forests, poses a threat to rare wood inhabiting fungi. Furthermore, in the past years several changes to the Forest Act gave preference to those using timber industrially. The additional need for large volumes of timber will only worsen this process.

Biodiversity 

In 2016 a study was published suggesting that intensive management of Estonian forests, especially spruce dominated forests, poses a threat to rare wood-dwelling fungi.

Even more threatened is the flying squirrel (Pteromys volans L.)  The population of this rare mammal, whose habitat ranges from the Baltic Sea in the west to the Pacific coast in the east, is decreasing with every passing year. The Alutaguse forest district, in the north-east of the county, is the last permanent habitat of Estonia’s most endangered animal, These animals favour old growth forests, and they are seen as in indicator of the quality and health of the habitat. In the early 1990s, the habitat of flying squirrels covered 3180 square kilometres, but this has now shrunk to 550, a decrease of more than 80% over the last twenty years. There are currently less than 40 nesting places of flying squirrels left.

Birds also suffer from the consequences of intensive logging. In January 2017, the Estonian Ornithological Society warned that between 1984 and 2016, the abundance of forest-related species has decreased by an average of 60,000 bird pairs per year (0.5%), due to changes to forestry legislation and intensified forest management, leading to significant negative impacts on Estonian forests.

Water management
The mill will be built near the major Estonian river Emajõgi and will not use totally chlorine free technology (TCF), nor a closed water cycle, putting at risk local water ecosystems, which are already under severe stress. The mill will discharge a huge amount of effluents (1.2 % of the river flow), containing chloride, potassium, carbon, calcium and sulphate ions, threatening the credibility of national plans to reduce the river pollution to meet European Union requirements, and causing further harm to the lake’s ecosystem (source: Report of the National Audit of Estonia).

Governance 

According to the TV station Pealtnägija show, the State Forest Agency RMK agreed with Est-For 15 years supply of timber. RMK was lead until December 2016 by an  Est-For investor, and father of Est-For representative, Mati Polli. He resigned just before the new mill project have been announced. According to the Pealtnägija show, the agreement between RMK and Est-For had been signed beforethe project was made public. It is not clear whether the deal had been initially agreed before or after Mati Polli’s resignation from RMK board, but critics note that in either case he could have had an undue influence.

In March 2018, the City Council of Tartu released a strong position statement opposing the project, drawn up by consensus by all political groups: "Due to the unlawfulness and questionability of current procedural steps, the implementation of a national special plan is forbidden and the procedure for the drawing up of a national special plan must be called off." Rural municipalities in Tartu County have voiced similar opinions, with seven out of its eight local governments following the city's move. The decision came after meetings with all stakeholders, including the company that is promoting the new mill. Despite strong local concerns, the government decided to move forward with the national designated spatial plan for the establishment of the infrastructure necessary for the operating of the Est-For pulp mill. The City Council of Tartu has announced that it will take action against that decision.