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This paper proposes an online estimation algorithm for the flow field in the proximal region about aquaculture fish-nets. The algorithm’s intended use is to provide a fast online estimator of local water flow field modifications caused by aquacultures. This information is required to improve the performance of feedback based control algorithms-particularly feedback linearization based controllers-for underwater robotic operations in the proximity of aquaculture structures. The algorithm makes use of a dynamic 3D fish-net model based on a lumped-mass method. The 3D model is augmented with potential panels and uses the panel method, to provide estimates of the flow velocity. The model is validated through several simulations for a small-scale open cylinder exposed to steady uniform current.