To find out more information on this matter, I decided to email the ADCNR/Wildlife and Freshwater Fisheries Division. Here is what they said:
No net loss of stream or wetland functions should occur as a result of the project. Adverse functional impacts may result from physical impacts to a stream or wetland, or from the alteration of a stream's natural flow regime or the impairment of wetland hydrology. Adverse stream impacts requiring mitigation may include accelerated siltation resulting from improper construction or erosion control practices, stream realignment, flow diversion or interruption, the placement of riprap or other fill in the streambed in such a way that habitat functions are impaired or fish movement is impeded under low flow conditions, and other modifications of habitat or hydrology which reduce the density or diversity of aquatic species. If flowing streams, ditches, or wetlands will be impacted by the proposed activity, the Mobile District, Army Corps of Engineers should be contacted at 251-690-3188 to determine if the activity falls under a Corps regulation requiring mitigation for adverse ecological, morphological, or hydrological impacts.