This article investigates water circulation in small-scale (~10 km²), shallow (less than 4 m) and micro-tidal estuaries. The research characterizes the hydrodynamic wind response in these domains using field data from Fangar Bay (Ebro Delta) jointly with three-dimensional numerical experiments in an idealized domain. During calm periods, field data in Fangar Bay show complex water circulation in the inner part of the estuary owing to its shallow depths and positive estuarine circulation in the mouth. Numerical experiments are conducted to investigate wind-induced water circulation due to laterally varying bathymetry. For intense up-bay wind conditions (wind intensities greater than 9 m·s⁻¹), an axially symmetric transverse structure occurs with outflow in the central channel axis and inflow in the lateral shallow areas. These numerical results explain the water circulation observed in Fangar Bay during strong wind episodes, highlighting the role of the bathymetry in a small-scale environment. During these episodes, the water column tends to homogenize rapidly in Fangar Bay, breaking the stratification and disrupting estuarine circulation, consistent with other observations in similar domains.