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Large floating dock systems consist of a complex arrangement of components whose environmental loading and movements can be challenging to predict due to interaction between elements. Recent advances in multi-physics Computational Fluid Dynamics (CFD) technology have allowed expansion of marine structure analysis from typical coastal engineering studies into a complete evaluation of dynamic system behavior by simulating inter-float and pile-float connection loadings. These recent advances have been applied to wave loading of several marine terminal facilities in San Francisco Bay, including the conceptual design for an interconnected concrete float system for the Water Emergency Transportation Authority’s (WETA) Central Bay Operations and Maintenance Facility (CBOM), to investigate system characteristics typically too complex to accurately evaluate. Results of this wave loading analysis demonstrate that guide pile stiffness and float connection rigidity can have a significant impact on load distribution within a float system which should be taken into consideration during design.