Extraction of natural gas from hard-to-reach reservoirs has expanded around the world and poses multiple environmental threats to surface waters. Improved drilling and extraction technology used to access low permeability natural gas requires millions of liters of water and a suite of chemicals that may be toxic to aquatic biota. There is growing concern among the scientific community and the general public that rapid and extensive natural gas development in the US could lead to degradation of natural resources. Gas wells are often close to surface waters that could be impacted by elevated sediment runoff from pipelines and roads, alteration of streamflow as a result of water extraction, and contamination from introduced chemicals or the resulting wastewater. However, the data required to fully understand these potential threats are currently lacking. Scientists therefore need to study the changes in ecosystem structure and function caused by natural gas extraction and to use such data to inform sound environmental policy.