Long-duration crewed space missions require bioregenerative life support solutions to improve mission sustainability and resiliency in the harsh environment of space. Understanding the impact of the space environment on Earth ecosystems is a critical next step in developing such solutions. This manuscript presents the experimental design of the SCAMPI Project (Saltwater Crustacean, Algae, and Microbe Population Investigation), a student mission to investigate the effect of microgravity and increased radiation on a multitrophic aquatic closed ecological system. The team is developing a custom payload, consisting of a sealed aquarium and instrumentation suite, to be integrated into the ICE Cubes facility onboard the International Space Station. Remote monitoring will collect data and imagery on the biotic and abiotic factors within the closed environment, informing a digital twin simulation that is being developed concurrently. This experiment will be the latest in a short list of ecosystem-scale experiments to fly in space, and address fundamental knowledge gaps including microbial community dynamics in microgravity. Ultimately, SCAMPI will provide data to inform the design of future closed ecological life support technologies by validating the hypothesis that Earth's ecosystems can function nominally in the space environment. The experiment is currently being built as a part of ESA's PETRI program and anticipates launching in early 2025.