Heavy ion accelerators are a valuable resource for the nuclear science community to study atomic physics. One such heavy ion accelerator is the Coupled Cyclotron Facility (CCF) at the National Superconducting Cyclotron Laboratory (NSCL) which relies on Electron Cyclotron Resonance (ECR) ion sources to provide the primary beam to the target. ECR ion sources are essential for the efficient operation of research accelerators such as the CCF, providing high currents of highly charged ions. Highly charged ion beams increase the efficiency of the accelerators, but require longer confinement times and higher temperature plasmas in the ion sources than is necessary to produce singly charged beams. The need to use high temperature and low density plasmas creates challenges including those relating to plasma stability. ECR ion sources provide a good platform to accept metallic vapor ovens and sputtering probes allowing the CCF to accelerate up to 30 types of beams ranging from oxygen to uranium. Furthermore, ECR ion sources use no filaments or cathodes providing a high degree of reliability for the accelerator facility. As the intensity frontier demands ever rarer isotopes from accelerator facilities, the heavy ion beam intensity must increase [70], which creates new demands from the ion sources.The work presented within this dissertation set out to better understand the mechanism that confines highly charged ions in the ECR plasma. Specifically, it was explored if hot electrons (energy larger than 50 keV) contribute to ion confinement by generating an electrostatic well in the plasma potential [68]. Perturbative measurements of ECR ion sources are presented with the aim to explore ion confinement times: pulsed sputtering (Chapter 4) and amplitude modulation (Chapter 5). Chapter 3 explores the geometry of the sputtering probe with respect to the magnetic field which was crucial to produce reliable pulsed sputtering results on the ECR ion source. Axial pulsed sputtering, which could be conveniently implemented on fully superconducting sources, incorporated a bias disc effect that highly perturbed the plasma. Radial sputtering was emulated by placing a semi-shielded probe along the plasma chamber wall in between the electron loss surfaces.Ion confinement time was characterized through the decay time of the beam current, which is proportional to ion confinement time. Ion beam decay times were measured for different charge states of gold in an oxygen plasma in Chapter 4. Decay time always increased with increasing charge state. Decay time also increased with hot electron temperature for lower frequency operation (13 GHz), but reached an optimized value for higher frequency operation (18 GHz) due to plasma instabilities. Electrostatic confinement of ions appeared to be the most plausible mechanism to explain the observed decay time behaviors. A novel perturbative measurement technique was developed for ECR ion sources using Amplitude Modulation (AM) of microwave power. The AM measurement was originally motivated by whether or not 50~kHz modulation in microwave power (from the microwave source) would be observable in the beam current. A systematic study was organized on the University of Jyvaskyla Physics Department (JYFL) normal conducting ECR ion source in Jyvaskyla Finland. Chapter 5 presents the beam current response to AM on the 14 GHz ECR ion source for different weights of noble gases, magnetic fields, and vacuum pressures. The beam current amplitude generally decayed exponentially for frequencies higher than around 400 Hz with the modulation highly suppressed at 10 kHz.