Quoted from: https://www.usgs.gov/software/mt3d-usgs-groundwater-solute-transport-simulator-modflow 

MT3D-USGS capabilities and features include:

• supports simulation of transport using MODFLOW 6 flow solution (structured grids only)
• unsaturated-zone transport;
• transport within streams and lakes, including solute exchange with connected groundwater;
• capability to route solute through dry cells that may occur in the Newton-Raphson formulation of MODFLOW (that is, MODFLOW-NWT);
• new chemical reaction package options that include the ability to simulate interspecies reactions and parent-daughter chain reactions;
• new pump-and-treat recirculation package that enables the simulation of dynamic recirculation with or without treatment for combinations of wells that are represented in the flow model, mimicking the above-ground treatment of extracted water;
• reformulation of the treatment of transient mass storage that improves conservation of mass and yields solutions for better agreement with analytical benchmarks;
• separate specification of the partitioning coefficient (Kd) within mobile and immobile domains;
• capability to assign prescribed concentrations to the top-most active layer;
• change in mass storage owing to the change in water volume now appears as its own budget item in the global mass balance summary;
• ability to ignore cross-dispersion terms;
• definition of Hydrocarbon Spill-Source Package (HSS) mass loading zones using regular and irregular polygons, in addition to the currently supported circular zones; and
• ability to specify an absolute minimum thickness rather than the default percent minimum thickness in dry-cell circumstances.

Download Current Version of MT3D-USGS

MT3D-USGS Version 1.1.0 06/28/2019 is the current release.

• MT3D-USGS Release Notes
• Summary of MT3D-USGS
• Readme and installation instructions
• MT3D-USGS program, source code, user guides, and example problems

Documentation for MT3D-USGS

Bedekar, V., Morway, E.D., Langevin, C.D., and Tonkin, M., 2016, MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW: U.S. Geological Survey Techniques and Methods 6-A53, 69 p., http://dx.doi.org/10.3133/tm6A53
This is the initial report that describes the theory and use of MT3D-USGS.

Superseded MT3D-USGS Versions

MT3D-USGS is not a replacement for MT3DMS. Separate updates to both codes will likely continue in the future. Therefore, MT3D users should check appropriate webpages for updates and releases of MT3D-USGS and MT3DMS separately. (MT3DMS is not a USGS software product; USGS cannot assist with MT3DMS questions or support.) The original MT3DMS software is available at http://hydro.geo.ua.edu/mt3d/

Find MODFLOW-Related Software

Visit the MODFLOW and Related Programs page for a list of MODFLOW-related software.

How to Cite MT3D-USGS

This USGS software has two citations associated with it.

1. The report citation is for the original report or article documenting the underlying theory, methods, instructions, and (or) applications at the time the initial version of the software was released. This digital object identifier (DOI) is for the report.
2. The software release citation is for the software/code itself (now referred to by USGS as a "Software Release") and references a specific version of the code and associated release date. This DOI links to the code.

In instances where an author is citing use of this software, it would be appropriate to cite both the report documenting the code and the specific software release version that was used.

Report Citation for MT3D-USGS

Bedekar, V., Morway, E.D., Langevin, C.D., and Tonkin, M., 2016, MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW: U.S. Geological Survey Techniques and Methods 6-A53, 69 p., http://dx.doi.org/10.3133/tm6A53

Software/Code Citation for MT3D-USGS v1.0.0

Bedekar, V., Morway, E.D., Langevin, C.D., and Tonkin, M., 2016, MT3D-USGS version 1.0.0: Groundwater Solute Transport Simulator for MODFLOW: U.S. Geological Survey Software Release, 30 September 2016, http://dx.doi.org/10.5066/F75T3HKD

Software License and Purchase Information

This software is a product of the U.S. Geological Survey, which is part of the U.S. Government.

Cost

This software is freely distributed. There is no fee to download and (or) use this software.

License

Users do not need a license or permission from the USGS to use this software. Users can download and install as many copies of the software as they need.

Public Domain

As a work of the United States Government, this USGS product is in the public domain within the United States. You can copy, modify, distribute, and perform the work, even for commercial purposes, all without asking permission. Additionally, USGS waives copyright and related rights in the work worldwide through CC0 1.0 Universal Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/ ).

SOFTWARE USER RIGHTS NOTICE

This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use. Also refer to the USGS Water Resources Software User Rights Notice for complete use, copyright, and distribution information.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.