The computational design of soft underwater swimmers is challenging because of the high degrees of freedom in soft-body modeling. In this paper, we present a differentiable pipeline for co-designing a soft swimmer's geometry and controller. Our pipeline unlocks gradient-based algorithms for discovering novel swimmer designs more efficiently than traditional gradient-free solutions. We propose Wasserstein barycenters as a basis for the geometric design of soft underwater swimmers since it is differentiable and can naturally interpolate between bio-inspired base shapes via optimal transport. By combining this design space with differentiable simulation and control, we can efficiently optimize a soft underwater swimmer's performance with fewer simulations than baseline methods. We demonstrate the efficacy of our method on various design problems such as fast, stable, and energy-efficient swimming and demonstrate applicability to multi-objective design.