Research has shown the highest level of understanding in the geosciences to be the ability to think about the Earth as a dynamic system (Stokes 2011). The Earth System contains four spheres: the geosphere, the hydrosphere, the biosphere, and the atmosphere. These spheres are linked through the biogeochemical cycles that move matter and energy through the various parts of the Earth System (Jacobson et al., 2000). Qualitative research has been done to understand undergraduate misconceptions in the geosciences (Arthurs, 2011), but there appears to be minimal work completed to examine students' alternate conceptions about biogeochemical cycles. This study aims to fill this gap by understanding how undergraduate students perceive fluxes and reservoirs of important elements within the Earth system; namely carbon, nitrogen, and phosphorus. Through interviews, concept drawings, and a questionnaire containing pilot assessment questions, undergraduate students' conceptions and alternate conceptions about the Earth System and biogeochemical cycles were collected. Using a constructivist grounded theory approach consisting of both semi-structured interviews and concept drawings, this data was analyzed to paint a fuller picture of what students know and what they think they know about both the Earth System and biogeochemical cycles. Additional data on courses students have taken across the sciences was also collected to give a glimpse at how Earth System thinking and biogeochemical cycles are being explicitly or implicitly taught both in and outside of the geosciences. The broader goal of this study is to use these alternate conceptions to inform the development of an instrument designed to measure Earth Systems thinking through the lens of biogeochemical cycling.