There are a host of regulations that protect sensitive areas. For example, prior to a natural gas operator constructing a well pad or pipeline, they are required by state law to conduct multiple environmental and wetland reviews to ensure there are not any threatened or endangered species in the area. As for best, or recommended practices, the Marcellus Shale Coalition has published a set of guidance documents for various aspects of development. To view these recommended practices, click HERE.
The American Petroleum Institute (API) also has a set of industry standards that are commonly implemented in well development.