By integrating the research and resources of hundreds of scientists from dozens of institutions, network-level science is fast becoming one scientific model of choice to address complex problems. In the pursuit to confront pressing environmental issues such as climate change, many scientists, practitioners, policy makers, and institutions are promoting network-level research that integrates the social and ecological sciences. To understand how this scientific trend is unfolding among rising scientists, we examined how graduate students experienced one such emergent social-ecological research initiative, Integrated Science for Society and Environment, within the large-scale, geographically distributed Long Term Ecological Research (LTER) Network. Through workshops, surveys, and interviews, we found that graduate students faced challenges in how they conceptualized and practiced social-ecological research within the LTER Network. We have presented these conceptual challenges at three scales: the individual/project, the LTER site, and the LTER Network. The level of student engagement with and knowledge of the LTER Network was varied, and students faced different institutional, cultural, and logistic barriers to practicing social-ecological research. These types of challenges are unlikely to be unique to LTER graduate students; thus, our findings are relevant to other scientific networks implementing new social-ecological research initiatives.