Ion cyclotron motion can play a role in shaping magnetospheres and governing magnetospheric dynamics, particularly in weakly magnetized systems such as the moons of outer planets. However, MHD explicitly neglects such effects. We demonstrate the importance of ion cyclotron motion in the near space environment of Ganymede using 3-dimensional multi-fluid simulations to account for Galileo magnetometer data from several flybys through various regions of Ganymede's magnetosphere. These simulations track several ion species and incorporate ion cyclotron effects through a comprehensive treatment of the plasma dynamics and the generalized Ohm's law equation. In the ideal MHD limit of the multi-fluid formulation the size of Ganymede's magnetosphere is underestimated, while in the full multi-fluid treatment the magnetosphere is shown to be in good agreement with magnetometer measurements from Galileo. The importance of treating the ion cyclotron motion is most noticeable near the magnetopause where magnetic field strengths approach zero.