Wells that are open to multiple aquifers can provide preferential pathways to flow and solute transport that short-circuit normal fluid flowlines. Representing these features in a regional flow model can produce a more realistic and reliable simulation model. This report describes modifications to the Multi-Node Well (MNW) Package of the U.S. Geological Survey (USGS) three-dimensional ground-water flow model (MODFLOW). The modifications build on a previous version and add several new features, processes, and input and output options. The input structure of the revised MNW (MNW2) is more well-centered than the original verion of MNW (MNW1) and allows the user to easily define hydraulic characteristics of each multi-node well. MNW2 also allows calculations of additional head changes due to partial penetration effects, flow into a borehole through a seepage face, changes in well discharge related to changes in lift for a given pump, and intraborehole flows with a pump intake located at any specified depth within the well. MNW2 also offers an improved capability to simulate nonvertical wells. A new output option allows selected multi-node wells to be designated as 'observation wells' for which changes in selected variables with time will be written to separate output files to facilitate postprocessing. MNW2 is compatible with the MODFLOW-2000 and MODFLOW-2005 versions of MODFLOW and with the version of MODFLOW that includes the Ground-Water Transport process (MODFLOW-GWT).