Two-dimensional (2D) van der Waals (vdW) materials offer easily tunable optical, electronic, and magnetic properties when compared to bulk systems. Layered 2D structures are free from interfacial strain and dangling bonds, and their ability to be interchangeably stacked enables flexible engineering of devices and novel correlated electronic states. Recently-discovered 2D magnetic materials have added an exciting design parameter to vdW heterostructures. As silicon-based transistors approach the limits of Moore’s law, 2D magnetic spintronics devices using both charge and spin current may spur a new generation of higher-efficiency electronics. In the 2D extreme, defects, strain, and other local variations can have strong impacts on overall properties. High-resolution and sensitive tools are needed to connect macroscopic behaviors to their origins in the microscopic structure. Scanning transmission electron microscopy (STEM) has been a successful 2D materials characterization method because of its sub-Angstrom resolution, wide variety of secondary signals, and increasing electron transmission for thinner specimens. In this dissertation I use Lorentz TEM and 4D-STEM electron diffraction techniques to address longstanding questions about structural and magnetic order in two 2D vdW magnetic systems. As a first topic, I investigate stacking polytypes in intermediate-thickness 2D CrI3 above and below the bulk structural transition temperature (Chapter 3). The interlayer registration in CrI3 determines its magnetic ordering, so understanding the structural phase space of few-layer CrI3 is essential to intentional magnetic design in 2D CrI3-based devices. I find that 2D CrI3, like bilayer CrI3, remains in a monoclinic symmetry at low temperature, but that there are significant mixtures of monoclinic stacking variants separated by domain walls that may disorder the magnetism. As a second topic, I image magnetic ordering in vanadium-doped WS2, demonstrating the first reported Lorentz TEM imaging of a monolayer magnet (Chapter 4). I find that Lorentz TEM contrast manifests unexpectedly in atomically-thin materials, as their flexural rigidity is low enough that they can be bent by the external magnetic field in the microscope. I also discuss the effects of the electron beam on carrier-mediated magnetic systems like dilute magnetic semiconductors, which may have important implications for future characterization of these materials for spintronics devices.