Ecosystems are affected by the physical perturbations of mining operations, as well as the chemical alterations in soil and water. Mining activities vary, but can include soil compaction and conversely, removal of the topsoil. These alterations disrupt nutrient dynamics by minimizing the availability of nitrogen and phosphorus, lower the pH through the acidification of the soil and can introduce toxic metals and acids. Depending on the scale and nature of the mining operation, these effects can be localized to the location of the mining or, through local hydrology, can extend to nearby aquatic systems, such as stream, wetlands and lakes.

Soil compaction is one of the most severe effects mining has on ecosystems. Compaction is often the result of bulldozers and other pieces of large machinery moving across the landscape, often for many years while the mining is still in operation. As the soil is compacted, there are fewer pore spaces for oxygen and water to move through the soil profile, minimizing the potential for plant establishment. Also, as water is unable to percolate down through the soil, it inevitably will move across the surface of the landscape and increase the possibility of contaminating nearby aquatic systems, such as wetlands, streams and lakes. Conversely, the topsoil, which is typically the top 30 cm of soil, can be mined. This lowers the overall fertility of the soil and increases water movement through the soil and landscape

Mining operations often contaminate the soil with toxic heavy metals and acids. Acids can lower the pH of the soil, preventing plants and soil microorganisms from thriving, and can also react with various minerals in the soil that are required by plants, such as calcium and magnesium. The hydrogen ions from the acid absorb the soil particles, preventing other nutrients required by plants to remain in the soil. These chemical alterations can interact with soil compaction. Because water isn't moving through the soil profile, some of the metals and acids can get carried away by the water, extending the mining effects throughout greater portions of the landscape. Elkins, Parker, Aldon and Whitford report in their article "Responses of Soil Biota to Organic Ammendments in Stripmine Spoils in Northwestern New Mexico," in the "Journal of Environmental Quality," 1984, that the addition of organic matter to mined lands can increase water retention in the soil, as well as the microbial process of nutrient accumulation and processing, potentially offsetting and minimizing the ecosystem effects from mining operations.

Ecosystems function because of the continuing interaction between the biotic (living) and abiotic (nonliving) components. Because each component affects how all others function, the depletion of soil nutrients and the acidification and compaction of the soil profile can limit the amount of plant life that can colonize a location. With reduced plant biomass, less carbon is being processed via photosynthesis, which leads to less oxygen production, less standing biomass and reduced transfer and cycling of nutrients. Also, plants are key regulators in an ecosystem's water cycling as they utilize moisture in photosynthesis and transpire water vapor back into the atmosphere. As such, the absence of plants in an ecosystem can inhibit the multiple functions and services commonly provided.