The Parallel Data Assimilation Framework (PDAF) is a widely used open-source software for data assimilation (DA) with complex, high-dimensional Earth system models and other applications for research and operational use. PDAF is structured to provide a framework for ensemble integrations and to assimilate observations. For the DA, it provides ensemble Kalman filters and smoothers, nonlinear ensemble DA methods, and 3D variational methods. PDAF's observation module interface (PDAF-OMI) further provides a system for structured observation handling, enabling the management of large numbers of different observation types. With the recent upgrade to version 3, PDAF underwent significant code modernization and functionality enhancements to unify more than 20 years of developments since its first release. This study provides a comprehensive overview of PDAF's functionality and concepts, including the new features introduced with the major revision. These are, in particular, a new universal interface that allows for the application of any ensemble filter and smoother method, or any 3D variational method, without changes to the source code. Further, a class of ensemble Kalman filters that processes observations serially, new diagnostics for the ensemble and observations, model-independent support for incremental analysis updating (IAU), and an explicit mode for file-based offline coupling between the model and the DA were added in the major revision. PDAF can apply the same DA methods to idealized toy models as well as realistic high-dimensional models without recoding. This speeds up the development and testing of new DA methods. The implementation of a DA system with PDAF is performed utilizing a set of template files. These allow for the implementation in a very limited time, supported by extensive documentation, as is demonstrated by an example implementation with a toy model. For high-dimensional applications, PDAF allows developers to start the implementation of a new DA system with low complexity and to extend its functionality stepwise, enabling an easy start with DA. Couplings to more than 30 models have been implemented by the PDAF developers and the user community and many of them are publicly available. Further, PDAF's internal interface to DA methods provides a clear approach to add new algorithms that can leverage PDAF's framework functionality for observations, localization, and state vector handling. This allows developers of DA methods to make their methods available to the PDAF community.