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To understand the fluid dynamics of marine phenomena fluid-structure interaction problems must be solved. Challenges exist in developing analytical and numerical methods to solve these complex flow problems. Specifically, handling the boundary conditions at fluid-structure (both solid and porous) interfaces is of critical importance in these problems. I will present details of two different problems where these challenges are handled: (1) modeling of marine aggregates settling in density stratified fluids and (2) modeling of pulsating soft corals. These problems will be motivated by field and experimental work in the marine sciences. I will discuss the related data and provide comparisons between this data and the models.