Quoted from: https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs?qt-science_center_objects=0#qt-science_center_objects
The USGS releases multiple versions of MODFLOW. This page focuses on MODFLOW versions that are part of USGS water enterprise software that is funded, developed, and maintained by the USGS Water Resources Mission Area. There is a core MODFLOW version, which is developed and maintained by the USGS Water Mission Area, and there are advanced versions. The core MODFLOW version is the one that is under active development and is often the most widely used and most thoroughly tested version. MODFLOW 6 is presently the core MODFLOW version distributed by the USGS, but MODFLOW-2005 (the previous core version) is still actively maintained and supported. Advanced MODFLOW versions include specialized MODFLOW variants and versions of MODFLOW that use newer formulations. These advanced MODFLOW versions are also available from the USGS.
There have been six major releases of the core MODFLOW version: MODFLOW-84, MODFLOW-88, MODFLOW-96, MODFLOW-2000, MODFLOW-2005, and MODFLOW 6. The first three versions of the code, MODFLOW-84, MODFLOW-88 and MODFLOW-96, were based on the initial conceptualization of the program as a groundwater-flow model only. Specific aspects of a groundwater-flow system are simulated by these codes by use of independent, modular-programming components called "Packages," such as the Well Package and River Package. MODFLOW's modular design was further expanded with the release of MODFLOW-2000 by the addition of "Processes," which are defined as parts of the code that solve a major equation or set of related equations and that consist of sets of the underlying packages. The part of the code that solves the groundwater-flow equation became the Groundwater Flow (GWF) Process. Although additional processes have been developed for MODFLOW, the GWF Process remains a core process on which other MODFLOW simulation capabilities are built. The primary change in MODFLOW-2005 from MODFLOW-2000 is the approach used by MODFLOW-2005 for managing internal data.
MODFLOW 6 is the newest core version and uses a new format of blocks and keywords for input of model data. It was written from scratch using an object-oriented design. MODFLOW 6 presently supports one type of process model — the GWF Model. Other models may be added in the future, such as a groundwater transport model, a surface-water model, and a pipe network model, for example. Underlying MODFLOW 6 is a framework that allows developers to add new models and the interactions between models. A key feature of the new MODFLOW 6 framework is the ability to solve multiple, tightly coupled, numerical models in a single system of equations. These may be multiple models of the same type or of different types. MODFLOW 6 is an entirely new version of MODFLOW.