Impact on Indigenous lands: In order to construct the waterway, the Tapajós river will have to be deepened and desilted so that ships can use it during all tides. Along the river from Santarém to Itaituba there are many traditional communities living and surviving from the river, and the construction of the waterway will destroy not only their sacred places but also put their survival at risk. Deepening the river will likely kill many fish, meaning that local communities will no longer be able to rely on fishing for their diet or livelihood.

The planned hydroelectric plants will have a devastating impact on the region, causing flooding of local communities' homes and sacred places. A total of 78'380 hectares (ha) in protected areas would be flooded and the Chacorão dam alone would inundate 18’700 ha of Munduruku Indigenous land. The impacts of dams at the top of the river affects the middle and lower regions of the river, as it is a living organism and should be treated as such, explain the people who live there. The communities speak from experience with previous dams, such as the Belo Monte Dam, which led to the reduction of protected areas, destruction of biodiversity, forced displacement of traditional communities, water pollution and subsequently a massive decline in subsistence fishing. 

Following opposition from indigenous peoples, the quilombos and the traditional communities, the São Luíz do Tapajós power plant had its licence suspended in 2016. However, the Tapajós people are aware that this is not the end for such projects and are concerned that conflict caused by these projects will have a huge impact on local communities. Indigenous communities continue to resist the planned hydropower projects and ensure that their rights are respected, including their right to Free, Prior and Informed Consent (FPIC) as set out in Convention 169 of the ILO and the United Nations Declaration on the Rights of Indigenous Peoples.

The Amazon's living forest usually acts as a carbon sink, sequestering CO2 and keeping it out of the atmosphere. Dams, especially in the tropics, are far from green: carbon dioxide and methane - a greenhouse gas more than 20 times as potent as CO2 - are both released in significant amounts from organic matter in submerged soils and decaying vegetation. Combined deforestation impacts, including that of the Tapajós Complex, can potentially push the whole system beyond the tipping point, the time at which the Amazon rainforest as a whole stops sucking carbon dioxide from the atmosphere and ceases being a carbon sink, and instead becomes a carbon source, sending the greenhouse gases long held in its trees into the sky.

The impacts in the region and on the Amazon rainforest as a whole are manifold.

Impacts on hydrologic resilience: One of the most immediate and direct effects of any dam is the obstruction of water: downstream flow, seasonal fluctuations, and natural flood pulses are all diminished and controlled by dams and reservoirs. Dams interrupt essential natural connections, blocking the flow of nutrients, sediments, and aquatic life between headwaters and river channels downstream.

Another impact is water table contamination, due to the concentration of mercury in the reservoirs. To make the river navigable with big ships, it will be necessary to dredge it, destroying all life in the water and around it. In a region where illegal gold mining is omnipresent, the risk is high that by dredging the riverbed, mercury in the riverbanks spreads further. Once consumed by fish, the toxin bio-accumulates up the food chain; those at the top, such as large predators and people, consume the highest quantities of this toxic metal which poses a serious health risk.

All of these negative hydrological impacts are compounded and magnified when multiple dams are built in series along the same river, or in a river system, which would happen all across the Tapajós Complex.

Impacts on biodiversity: Construction of the dam would have profound effects on the species living within the freshwater ecosystem: big diversity losses for native aquatic species and the shrinking of Conservation Units, stemming from connectivity and water chemistry changes.

Philip Fearnside of the Instituto Nacional de Pesquisas da Amazônia (INPA), an Amazonian dam expert, explains that when free-flowing rivers are transformed into standing water, most of the range of species adjusted to the old currents, water composition, and flow is wiped out. That fact is chilling, considering that the Tapajós is home to 325 fish species alone, 65 of which are endemic.

Changes in fish populations will be felt by their predators, including two species of river dolphin (tucuxi and pink river dolphins). Freshwater dolphins also risk population fragmentation and isolation by some of the planned dams. Not only dolphins, but turtles will lose habitats and nesting beaches to dam reservoirs. Some species, such as the giant Amazon river turtle migrate hundreds of kilometres to return to their historic nesting beaches over their 80-100 year lifespans. The destruction of these sites will affect the integrity of these populations and disrupt the ability of the species to find mates.

Furthermore, several threatened species in the region will be affected including the giant armadillo, giant anteater, white-cheeked spider monkey, and oncilla (little spotted cat).

It is unclear which impact the different dams together might have on the region, since impact assessments have only been carried out for each project separately. However, risks are high that the sum of adverse impacts is much higher than estimated single impacts.

Although the Brazilian government have not included the project in its National Energy Plan by 2030 (PDE 2030) and licences for the project have not been granted, affected communities are on high alert due to the unpredictable actions of the government. They are concerned that the project will be developed despite its impacts on local communities and the environment.