I am not an expert on environmental issues, nor on the Amazon specifically. From what I have read, however, humans are the primary reason for the decline of the Amazon's reach. This is due to a multitude of things - not only deforestation (which is probably the biggest culprit) but also pollution and climate change.
The sediments of the Amazon Basin rendered the highway unstable and subject to inundation during heavy rains, blocking traffic and leaving crops to rot. Harvest yields for poor farmers were dismal due to poor training and inadequate soils, which were quickly exhausted necessitating more forest clearing.. Logging was difficult due to the low density of commercially exploitable trees. Rampant erosion, up to 40 tons of soil per acre (100 tons/ha) occurred after clearing. Many colonists, unfamiliar with banking and lured by easy credit, went deep into debt. Adding to the debacle was the environmental cost of the project. After the construction of the Trans-Amazonian Highway, Brazilian deforestation accelerated to levels never before seen.
Deforestation is a constant problem in the Amazon. The people who go there to mine trees just want to get everything they can get. They don't really care if there are any trees left at the end of the day. There is not enough law enforcement to protect the Amazon so its numbers are dwindling.
Most of the rivers in the world are actually dry river beds. A permanent river, such as the Amazon, retains its levels through a delicate balance of rain in its watershed, thirsty plants along its banks, and a controlled outflow. Rain, we know, originates from one of two sources: evaporation from the ocean, or plant transpiration. The Amazon watershed (the westmost part of the Amazon Rainforest) is blocked off from the Pacific Ocean by the Andes mountains, so its only source of water comes from plant transpiration. It logically follows that reducing the number of plants reduces the rain in the watershed, and therefore the amount of water in the river.