The spread of agriculture led to deforestation and more water usage through irrigation as well as salinization. The "fertile crescent" in the Tigris-Euphrates area lost most of its trees to farming, causing erosion and frequent flooding. The population also drastically increased with more food under cultivation putting more strain on other resources. The first city of Uruk collapsed after over-planting, over-populating the area. As a result the soil was exhausted. Nothing grows there now--the site of the first city in human history looks like the surface of the moon today. As Jared Diamond explained: "Deforestation led to soil erosion, and irrigation agriculture led to salinization, both by releasing salt buried deep in the ground and by adding salt through irrigation water. After centuries of degradation, areas of Iraq that formerly supported productive irrigation agriculture are today salt pans where nothing grows."
See Jared Diamond, The Erosion of Civilizations," LA Times (June 15, 2003).
The same happened to the ancient Nazca civilization of Ancient Peru--clearing forests, changed climate patterns, making the soil dryer and less able to support farming and life. The deep roots of trees helped hold the soil in place. The Nazca people cut them down to plant cotton and corn--these plants have shallow root systems allowing much of the soil to be washed away or blow away by the wind. This area, like the fertile crescent is dry and desert-like today.
See Rory Carroll, "Ancient Peruvian Nazca turned land to desert" The Guardian (November 1, 2009)