We present a synthesis of the first 10 years of Long Term Ecological Research project in Amazonian Forest. We elucidate the natural dynamics of forest ecosystem processes and associated biota, and its changes caused by distinct pressures of selective timber extraction and forest fragmentation. We found that, for both plants and animals, densities of individuals and distribution of species assemblages are spatially heterogeneous in the mesoscale, even in relatively undisturbed forests, and that associations with topo-edaphic variables allow prediction of a considerable part of this variation. For biological groups whose dynamics were studied in the short-term, levels of change in species composition and densities were relatively high, and these changes were generally in tune with spatial environmental variation. The impact of selective logging on assemblages and ecosystem processes was normally moderate, and around 19 years were needed for recovering forest biomass and tree size distribution. Continued studies are needed to determine the time required for recuperation of timber stocks and pre-logging floristic composition. Selective logging appears to be compatible with the biodiversity conservation, but reduction and better planning of roads access may be more important than planned logging intensities. Habitat loss’ impact on organisms and ecosystem processes is large and long-lasting, once it induces the privation of many taxonomic groups’ species, higher tree mortality and accelerated forest dynamics. There was a negative synergy between the impacts of habitat loss and climatic changes, and a better understanding of these processes can only be obtained through long-term research.