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Municipal intakes of surface water have various uses, and their impacts on the aquatic environment and ecosystem, such as the impingement and entrainment of ichthyoplankton, are a major concern. A robust assessment of the intake impacts on ichthyoplankton in a system generally requires modeling efforts that can simulate the transport and dispersal pathways of the ichthyoplankton. However, it is challenging to simulate hydrodynamics with a high-resolution grid at the scale needed for intake screen sizes in a large system. In this study, a 3D unstructured grid model with a fine resolution grid (<1 m) was developed to investigate potential impacts of an intake on aquatic resources in a tidal freshwater estuary. This approach enables us to directly estimate intake-induced mortality. With the use of the coupled particle-tracking model, we evaluated the total and maximum daily removal rates of particles by the intake that can be used to estimate percent mortality of ichthyoplankton. We further investigated how impacts from the intake vary with spawning locations, flow conditions, and vertical migration velocity of ichthyoplankton. A risk assessment was conducted based on designed flow of water withdrawals. This approach is widely applicable and can address impacts of water intakes in other systems. [ABSTRACT FROM AUTHOR]