Far from the surface, the ocean's midwater present a rich frontier of biodiversity that is not well understood. Part of this gap in our knowledge is the great expense involved in collecting data with remotely operated vehicles. In this presentation, we will discuss the pipeline of developing in-silico computational experiments in concert with in-situ experimental data. Using a combination of particle image velocimetry data, optical scans, and confocal microscopy, we will discuss the creation of fluid-structure interaction models for organismal pumping and fluid transport, with the goal of developing an intuition on the physical mechanisms that drive their success. Using a combination of simplified geometries and scanned body meshes, we will employ the immersed boundary/finite element (IB/FE) method to simulate chambered, valveless pumping mechanism generated by the pelagic tunicate known as a larvacean. Additionally, we will use the same modeling methodology to explore the metachronal motion and fluid transport of the parapodial paddles of the pelagic, midwater polychaete known as tomopterids. All motion described in these systems will not be prescribed and will emerge from the interaction of active muscular tension, passive elastic recoil, and the local fluid environment.