Abstract The Amazon watershed harbors a megadiversity of terrestrial and aquatic plants and animals. Mechanisms that sustain this biodiversity are the water level fluctuations the fluvial dynamics and the intense gene flux due to permanent integration of climatological, geomorphological and biological components of the system. The construction of hydroelectric reservoirs to support economic development of Brazil and other countries that share the Amazon basin will interfere with the ecological dynamics of this ecosystem changing the hydrological, hydrosocial and fundamental processes. Furthermore the construction of Andean reservoirs can disrupt the connectivity with the lower Amazon ecosystem. Principles of ecohydrologies, ecological engineering and preservation of key river basins, have to be applied in order to optimize energy production and promote conservation practices. Long term planning and integration of countries that share the Amazon basin is a strategic decision to control and develop the hydropower exploitation in the region.