While there is a small but growing body of literature on how novice teachers can be better prepared to improve instructional experiences for Emergent Bilingual Learners (EBLs) in science classrooms, very little is known about how secondary science teachers make sense of their ability to enact agency (as responsive practice for EBLs) within rigid schooling contexts (Authors, 2018). We analyze the discursive positionings of five novice teachers across 3 different university teacher education programs to explore how they perceive their agency, defined as their ability to effect change in EBLs’ opportunities to learn, and how they understand the systemic contexts of oppression which complicate their agency. We then discuss how preservice teachers experience or manage tensions of working within this complex structure/agency dialectic. We reflect on their experiences as a form of praxis crisis, i.e., the disjuncture between theory and practice that occurs as they negotiate the real constraints of their work. Finally, we articulate implications for ‘staying with the trouble’ (Haraway, 2016) in teacher education research and practice on science for EBLs.