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Research into the geometric nests built by white-spotted pufferfish indicated the nest’s potential for flow control and reduction in flow velocity. However, studies to date have only focused on the construction process and behaviour of the male pufferfish. Hence, the form and functions of the unique features of the nest remain unclear. The present study aims to explore the flow features most useful in understanding the habitat conditions of the nest through a combination of photogrammetric reconstructions of the nest features and two-dimensional (2D) computational fluid dynamic simulations. The findings show the role of the nest structure in reducing the flow velocity and shear stress within the nesting site. Analysis of shear stress indicates that male pufferfish build the outer zones of the nest with coarser material that improves the overall shear strength of these areas. The study identified the function of the nest structure in the protection of the eggs through reduction in flow variations and improved aeration. The addition of shell fragments to the nest peaks by the male pufferfish contributes to the resiliency of the nest structure and ensures a stable bed surface at the central zone.