Scientific open-source software (scientific OSS) has facilitated scientific research due to its transparent and collaborative nature. The sustainability of such software is becoming crucial given its pivotal role in scientific endeavors. While past research has proposed strategies for the sustainability of the scientific software or in general OSS communities in isolation, it remains unclear when the two scenarios are merged if these approaches are directly applicable to developing scientific OSS. In this research, we propose to investigate the unique challenges in sustaining the scientific OSS ecosystems. We first conduct a case study to empirically understand the interdisciplinary team’s collaboration in scientific OSS ecosystems and identify the collaboration challenges. Further, to generalize our findings, we plan to conduct a large-scale quantitative study in broader scientific OSS ecosystems to identify the cross-project collaboration inefficiencies. Finally, we would like to design and develop interventions to mitigate the problems identified.