For decades, molecular visualization software has been fundamental to education and research in chemistry, structural biology, and materials science. These tools have enabled the inspection of structures, dynamics, and interactions, yet their reliance on two-dimensional (2D) interfaces imposes persistent limitations. Traditional screen–mouse systems are poorly suited to conveying the inherently three-dimensional (3D) nature of molecules, and thoughtful manipulation of structures remains cumbersome even for expert users. Such barriers are particularly acute for students and occasional users, for whom intuitive understanding is critical. Immersive technologies under the umbrella of eXtended Reality (XR)—including Augmented Reality (AR) and Virtual Reality (VR)—offer a paradigm shift. By situating molecules directly in 3D space, XR facilitates both perception and manipulation, making abstract concepts more tangible. Educational benefits include heightened engagement and improved spatial reasoning, while for research XR offers more fluid collaborative exploration of molecular systems. Historically, adoption was limited by expensive, bulky hardware and complex software installation. The WebXR standard now addresses these issues by enabling cross-platform immersive experiences directly through browsers, eliminating installation barriers and improving accessibility. The MolecularWeb ecosystem (https://molecularweb.org) exploits these advances to deliver immersive molecular graphics and modeling widely. Its first platform, moleculARweb, brings “commodity AR” to everyday devices such as laptops and smartphones. Using simple fiducial markers or markerless AR, students can view and manipulate molecular structures in real time. Modules cover orbitals, VSEPR geometries, hydrogen bonding, and biomolecular assemblies, while Virtual Modeling Kits provide rudimentary molecular mechanics. Teachers report that these activities improve engagement and help clarify difficult concepts. To expand flexibility, the companion tool PDB2AR allows users to generate custom AR/VR scenes from Protein Data Bank entries, AlphaFold models, or objects exported from visualization software. These can be explored in stand-alone AR/VR or within MolecularWebXR, a multiuser immersive platform. MolecularWebXR provides shared virtual rooms where participants, represented as avatars, can examine curated content on chemistry, materials, and biology, or import their own structures. This framework has been deployed in classrooms, outreach events, and scientific meetings, highlighting its value as a medium for collaborative discussion. The most recent development, HandMol, moves beyond static visualization. Its prototypes enable multiuser, bare-handed manipulation of molecular structures with real-time feedback from molecular mechanics engines. Features include on-the-fly minimization, collaborative docking, seamless file exchange, and natural language control through language models. Soon to be integrated into MolecularWebXR, HandMol transforms immersive visualization into an interactive modeling environment suitable for both education and research. Together, these tools illustrate the progression from 2D visualization to dynamic, collaborative XR systems. By harnessing web technologies and integrating physics-based modeling with AI, the MolecularWeb ecosystem makes immersive molecular science broadly accessible, offering a glimpse of a future where teaching, learning, and discovery are more intuitive and interactive.