System modelling is an important task for the evaluation of measurement and experiment performance as well as budget control on system level. Space environmental effects and internal effects such as heat dissipation or magnetic fields induced by electric currents posses a considerable influence on payloads and experiments. In order to analyze and mitigate sources of disturbances with respect to the specified mission and payload requirements, we develop detailed finite element models of satellite systems and implement thermal, structural and magnetic analysis in conjunction with our orbit propagation tool thus providing realistic environmental boundaries as basis for the analyses. Depending on the level of the intended analyses we can focus on specific components, regarding the system as environmental boundary or evaluate the system as a whole including the dynamic influence of the space environment.