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The Ico-Mandantes Bay is one of the major branches of the Itaparica Reservoir (Sub-Middle SAo Francisco River, Northeast Brazil) and is the focus of this study. Besides the harmful algae blooms (HAB) and a severe prolonged drought, the bay has a strategic importancee.g., the eastern channel of the newly built water diversion will withdraw water from it (drinking water). This article presents the implementation of a three-dimensional (3D) numerical modelpioneering for the regionusing TELEMAC-3D. The aim was to investigate the 3D flows induced by moderate or extreme winds as well as by heating of the water surface. The findings showed that a windstorm increased the flow velocities (at least one order of magnitude, i.e., up to 10(-1)-10(-2) m/s) without altering significantly the circulation patterns; this occurred substantially for the heating scenario, which had, in contrast, a lower effect on velocities. In terms of the bay’s management, the main implications are: (1) the withdrawals for drinking water and irrigation agriculture should stop working during windstorms and at least three days afterwards; (2) a heating of the water surface would likely increase the risk of development of HAB in the shallow areas, so that further assessments with a water quality module are needed to support advanced remediation measures; (3) the 3D model proves to be a necessary tool to identify high risk contamination areas e.g., for installation of new aquaculture systems.