This study explores middle school student learning of Next Generation Science Standards aligned content and practices associated with use of an innovative virtual learning environment. The learning environment, a computer-based game called Mission HydroSci (MHS), was developed with the aim of supporting student learning of water systems science along with the practice of scientific argumentation. Teachers implemented MHS within their science classrooms as a replacement unit for water science over a period of two weeks. Pre- and post-test data were collected from 633 students across ten schools. Data included an assessment of water systems content and a test of argumentation competencies. Students demonstrated positive and statistically significant changes in water systems understandings and argumentation; however, the effect sizes were modest. These results have informed several revisions to the MHS learning environment including modifications to the argumentation platform within the game and additional attention to key water systems concepts.