Eight spacecraft have now visited the Jovian system and obtained a wealth of information about Jupiter's magnetosphere and aurora, both of which have proved to be very different from what we observe at the Earth. These differences are due in part to unique features such as large magnetospheric scale sizes, an internal plasma source from the moon Io, and a rapid planetary rotation period. These features have important influences on Jupiter's magnetosphere structure and dynamics, which are the focus of the three studies described in this dissertation. The first study is a survey of magnetometer data from the Jovian magnetotail to search for signatures of magnetic reconnection, an important dynamic process in planetary magnetospheres. Reconnection is thought to be predominantly internally driven at Jupiter. We have identified 249 reconnection events from the magnetometer data, and have analyzed their spatial distribution and periodicity to establish where and how often reconnection occurs at Jupiter. Results, including the location of a statistical separatrix, are compared to previous studies of flow bursts and particle anisotropies. The second study establishes a new model for relating auroral features to sources in the middle and outer magnetosphere. At Jupiter the polar aurora mapping is highly uncertain because global field models are inaccurate beyond ~30 Jovian radii. The open/closed field line boundary is also not well defined because Jupiter's main auroral emissions are associated with the breakdown of plasma corotation rather than the polar cap. Therefore our mapping model, which uses a flux equivalence calculation rather than tracing global models, provides a more precise mapping of the polar aurora and allows us to identify the size and location of Jupiter's polar cap. In the final study, we use a large scale kinetic simulation to examine the effects of centrifugal forces arising from Jupiter's rapid rotation and non-adiabatic field line stretching in the noon to dusk local time sector. We examine changes to the pitch angle and energy distributions and conclude that the changes arising from the non-adiabatic stretching effects could account for the field dipolarization and plasma sheet thickening observed between noon and dusk.