This is an excellent question, and it has been tackled recently by environmental historians. Specifically, historian William Cronon’s Changes in the Land looks at the ways in which colonial landscapes in New England assumed new meanings whenever Europeans began to colonize the region. The introduction and development of the land by Europeans initiated a fundamental change in the New England countryside. As Cronon states,
The replacement of Indians by predominantly European populations in New England was as much an ecological as a cultural revolution, and the human side of that revolution cannot be fully understood until it is embedded in the ecological one. (6)
Native Americans, Cronon argues, lived in a harmonious relationship with the landscape and the seasonal processes that renewed its vital forces. The Wampanoags, Powhatans, Pequots, and other New England tribes would fish in the spring and summer when the river fresh waters had just thawed while following the ever-migrating herds of deer and other small game. Their understanding of the landscape was built into the natural cycles of the seasons and New-England ecology itself, which gave them little need to commodify the things they hunted or establish concrete property relations.
Cronon continues that when the Europeans arrived, they brought with them all of the material relationships that had defined the development of western civilization for the previous 300 years. Rather than being contiguous, shared zones of natural plenty, whose resources vacillated with the vagaries of the seasons, plots of land, to European settlers, were divided up and turned into isolatable units of property. The value of the landscape no longer came from its connection to the larger natural universe but rather from its ability to be broken down into individual units that could be owned, cultivated, and sold on the European markets of the Old World. It was an incongruous way of thinking in comparison with Native American values.
Cronon’s case study of the changes that occurred in the New England landscape is undoubtedly the most famous explanation of the phenomenon you are describing in your question. Europeans came to the New World with an enormous socio-cultural baggage that they used to characterize and categorize the landscapes that they inhabited. The natives had no way of comprehending the European worldview, and they gradually saw their landscapes desiccated by such practices.