People have been extracting resources from the earth forever. From the first human that built a fire or killed an animal to modern extraction of hydrogen for rocket fuel. It's what people do. Some of these activities have minimal impact or might be considered natural and even beneficial. Paleolithic humans hunting for food may have caused the extinction of animals in Siberia and North America, but extinctions are a natural part of life on earth and for each extinction there leaves a place for some other animal or plant to take its place.
American Indians set wild fires to help them hunt destroying grasslands in large swaths, but the grass fires return nutrients to the soil and increase growth rates of new grass benefiting both grass and grazers and is integral to modern land management. In more recent times people have become more numerous and demanding, and have tools much more effective to extract and process natural resources.
Agriculture, hunting, fishing, and forestry are examples of resources that if managed properly can have a minimum of negative impact on our environment. Poor agriculture processes can lead to loss of usable land, and the pollution of water supplies from fertilizer and pesticide runoff. Deforestation can lead to land erosion and removes habitat for many forest species. Overfishing and fishing down the food chain, can leave us without fish in the future.
Mining for metals or coal has left great scars on the land from open pit mining. Tunneling leaves heaps of sterile tailings and when the mines are abandoned can pollute ground water for generations. Metals mining and refining, along with other industrial processes have polluted many streams. Take a look at this guide published by the state of Michigan concerning eating fish caught there.
The direct effects of petroleum extraction on the environment are limited to land subsidence when the oil is at shallow depth or visual harm from the drilling rigs or pumping facilities. The indirect effects are much more devastating to the environment, from the effluent of processing facilities to accidents such as the Exxon Valdez or BP’s Deep Water Horizon and intentional spills caused by human conflict, like the Kuwait war. Oil spills on the land surface can render the land unusable for humans and harmful to plants and the animals that depend on them. Spills on water kill birds and marine mammals in large numbers immediately from contact, and have longer term effects on fish stocks and aquatic life, detailed in this report.
Renewable sources of energy such as wind power or water power can have negative effects. Hydroelectric dams can supply cheap electricity and water for cities and agriculture, but render useless the land in the valley that existed before the dam was built. Dams in the northwest United States had a huge impact on salmon populations in the area. Wind generators are considered unsightly by residents and accused of having a negative impact on the environment in Nantucket Sound in Massachusetts.
Humans are a part of the environment, they always have been and always will be. Everything they do can have negative impact on the environment, and all of what they do will impact the environment in some way.