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.

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.

Water management
The mill will be built beside the river Emajõgi that flows into the trans-boundary Lake Peipus, on the Russian border, which is already in a poor condition. Its border location already creates challenges for its protection and restoration. The new mill will add further harm to the lake’s ecosystem due to use of its water and release of waste water in the river (source: Report of the National Audit of Estonia).