NHD stands for National Hydrography Dataset and is the surface water component of the United States Geologial Survey's National Map. The NHD datasets include a wide variety of layers and there are multiple versions and multiple download sources. In the context of BRAT, there are three primary layers we are after:
You don't have to use NHD or any specific version of NHD to run BRAT. As long as you can get a drainage network layer (whether you download it or derive it yourself), you can run BRAT. However, for most applications we reccomend using NHDPlus Version 2.1 , which (as of 2013) is the most current version of the NHD. You can download the original NHD data files here from the USGS among many other sites. However, we have found it easiest and fasted to download NHDPlus version 2.1 from here.
The video below walks you through the download.