Water as a refrigerant (R-718) for chiller and heat pump applications is gaining importance due to its environmentally friendly properties and wide availability. Nevertheless, water operates under atmospheric pressure below 100 °C and requires relatively high-volume flows. Both can be ensured using a screw spindle compressor with high rotational speeds. However, such high-speed applications introduce the risk of resonances, which can lead to operational failure if not correctly accounted for. In this study, the rotors’ dynamic behaviour of a screw spindle compressor assembly will be analysed by calculating its torsional and bending eigenfrequencies. The initial phase involves the determination of these natural frequencies for the standard assembly configuration. A case study is then conducted, varying the design and materials of the rotor assembly and reanalysing the eigenfrequencies to explore the influence of these modifications on the structural performance. Additionally, the excitation sources during the compressor's operation are identified, and a Campbell diagram is used to visualise potential resonances and critical speeds of the presented assemblies.