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This manuscript describes the development of a Matlab code along with a set of graphical user interfaces (GUIs) in order to conduct water budget and rainfall analysis for Southern Miami- Dade County Watershed. The model results provided spatial distribution of the water budget flow components that might be used to support the establishment of the technical criteria for minimum flows to Biscayne Bay to meet the requirement of the Florida legislature. In addition to providing a better understanding of the hydrology and water management of the region, the results of the water budget and rainfall analysis, conducted herein, were used to establish the boundary conditions for the hydrodynamic numerical model of the Biscayne Bay.