We investigate the ion population and energy distribution within Ganymede’s magnetosphere by examining Ganymede’s ionospheric outflow as a source of heavy (O+) and light (H+) ions and the Jovian magnetospheric plasma as an external source of heavy ions. We develop a method for examining the energy distributions of each ion species in a three‐dimensional multifluid simulation in a way directly comparable to the observations of the Plasma Experiment on the Galileo spacecraft. This is used to provide new insight to the existing controversy over the composition of Ganymede’s observed ionospheric outflow, and enables further examination of the energetic signatures of the ion population trapped within Ganymede’s magnetosphere. The model‐predicted ionospheric outflow is consistent with the in situ ion energy spectrograms observed by the Galileo Plasma Experiment at closest approach, and requires that both ionospheric H+ and O+ are present in the population of ions exiting Ganymede’s ionosphere over the polar cap. The outward flux of ionospheric ions was calculated to be ~1026 ions/cm2/s, which is in agreement with independently calculated sputtering rates of Ganymede’s icy surface. The modeled spectrograms define characteristic energy signatures and populations for various regions of Ganymede’s magnetosphere, which illustrate the major sources of ions trapped within the magnetosphere are Ganymede’s ionospheric O+ and H+. The fact that very little plasma was observed inside Ganymede’s magnetosphere during the G8 flyby is attributed to the region being shadowed from the sun for ~60 h, which may indicate the importance of photoionization for sustaining Ganymede’s ionospheric plasma source.