According to the project Environmental Impact Assessment (EIA), some 3,000 people will be forced to move from their homes, although judging from past dam projects in Brazil, this number is probably an underestimate. The decline in fisheries will seriously affect commercial and subsistence fishermen. Thousands of people living downstream will face declining crop yields as a result of the loss of the annual deposition of fertile silt on the flood plains,will be deprived of transportation and run the risk of mercury contamination.

Indigenous groups will be affected by thousands of migrants arriving in search of work on construction crews. Public health impacts in a region where malaria and other tropical diseases are endemic are likely to be substantial, with stagnant pools of water providing breeding grounds for mosquitoes and other disease-carrying insects.A study in august 2009 from the health and environmental department in Porto Velho, Rondônia, showed that since the construction of Jirau’s plant began malaria incidents have increased 63,6%.

Furthermore, there are signs that indicate the presence of isolated indigenous groups in the area to be flooded by the dams.

The region is a treasure of biodiversity. The Madeira River supports the life of an estimated 750 fish species, 800 bird species, and other endangered rainforest wildlife, and is home to rubber tappers, Brazil nut gatherers, and fishermen. Protected areas, including a reserve used by people who extract natural forest products, will be inundated by the dams.

The Madeira River project will further contribute to the fragmentation of Rondônia's ecosystems and to the clearing of vast areas of the region's remaining forests. A 600% increase in deforestation rates over last year was already reported in the area surrounding the Rio Madeira, after the preliminary license for the dams was granted in July 2007. The dams will seriously affect migratory fish and other aquatic species on the Madeira. Several species of large catfish migrate some 4,500 km each year to the upper Madeira to reproduce. Construction of the dams will block these migration routes, affecting the survival of the catfish. In addition, the dams are likely to cause more flooding than expected due to the huge amount of sediments carried by the Madeira river (around 500 million tons/year, equivalent to all other rivers in the Amazon basin) and cause the disruption to 33 endangered mammal species that are found in the project area.

Many suspect that the project sponsors are after something more ambitious: opening the upper Madeira to navigation by fitting the dams with locks. The extra cost would be small. Lower transportation costs would encourage farmers to plant much more soya and grains - at the expense of the remaining forest.

Large dams in the rainforest also emit enormous quantities of greenhouse gases, including methane, contributing to global warming.

Bolivian organizations filed a complaint at the Organization of American States (OAS) alleging violation of human rights, such as the right for information, due to Brazilian government's reluctance to consult the government of the neighboring country and perform studies to assess potential trans-boundary impacts of the Madeira River dams.

Populations living in the area affected by the dams say they have been pressured by the companies to move,despite the fact that they have not come to agreements regarding compensation and resettlement.

Violations of Brazilian and international labor legislation have already occurred since irregular working conditions at a construction site associated with Jirau’s plant have been confirmed. Moreover, also in September, workers at the Jirau’s construction site decided to strike for better payment and working conditions. 

The World Commission on Dams found that women and ethnic minorities were disproportionately affected by dam projects. As women are often responsible for ensuring the sustainable livelihoods of their families, impacts on these livelihoods through destruction of fisheries, flooding of agricultural land and forests, and displacement often result in women bearing a disproportionate share of the costs. It is women who are often left with the burden of caring for their families, finding alternative land and water sources and alternative livelihoods when these are taken away through the development of destructive dam projects.