Mining disturbs and removes the rocks, ores and minerals, sometimes leaving huge gaping holes in the earth. The mine tailings are piled up in large mounds on the surface of the lithosphere.

Mining waste can be washed into the waterways that are nearby and pollute the hydrosphere. The mine itself will sometimes fill up with water creating its own little hydrosphere complete with plant and animal life. 

Mining causes air pollution to the atmosphere in several ways. The equipment that digs the mine and extracts the ore or minerals is usually powered by fossil fuels such as diesel or gasoline engines. The mine might also release poisonous gases that were trapped below the surface. If the mine is a coal mine, then burning that coal pollutes the atmosphere long after the mining process is complete, further polluting the atmosphere. 

Mining affects the atmosphere by affecting the other three spheres in a negative way. The pollution from mining can cause birth defects in animals and humans. Trees, shrubs, grasses and other plants are killed directly and indirectly during the mining process.

Hope this helps!