The study reported in the paper has focused on the identification and analysis of various causal linkages that exist in the soft systems that operate within a larger R&D organizational system and the development of a system dynamics model based on these linkages. The Council of Scientific and Industrial Research (CSIR), a public-funded R&D organizational system in India with its constituent laboratories, has been considered for the study. Multiple regression analysis was employed to understand the influence of integration, coordination, and interdependence of research units or groups on quality performance of these units working in CSIR laboratories. In another study, the multivariate relationships between the availability of resources (material, human, organizational), and R&D effectiveness of research units were explored. Two other sets of studies were carried out to complement the above. In the first study, the factors and forces that motivate the scientists in the R&D work situations and those that contribute to the overall satisfaction of the scientists with their work groups were explored. The second study has assessed the use of mental energy by scientific personnel working in three CSIR laboratories with the objective of increasing the energy count for improving organizational effectiveness. Finally, a system dynamics model incorporating these feedback influences has been developed for the overall R&D organizational system.