Santa Catarina Island bays (SCI bays) has a great economic and social importance in the region. With more than 700.000 habitants in its surroundings, besides touristic and fishery activities, it represents approximately 70% of the Brazilian bivalve shellfish production. In order to understand processes controlling the water quality and food availability, relevant for the shellfish production, it is unquestionably important to understand the main hydrodynamics patterns of SCI Bay. Thus, a hydrodynamic assessment study of the SCI bays was carried out using the numerical model MOHID. The model was implemented using bathymetric information obtained from Brazilian nautical charts, two tide gauges in each one of the bays entrances and two meteorological stations. The fresh water input flow from affluent streams was discretized into 47 major catchments, representing total average flow of approximately 32 m3.s-1. An acoustic Doppler current profiler (ADCP) was deployed in two different locations, during a period of 28 days each, in order to obtain a time series of currents velocity and direction, which were then used to validate the model. An assessment of the model outputs using astronomical tides and measured tides is in development to evaluate the meteorological tide influence. Preliminary results using measured tide show correlation coefficients for water level of 0.95 and mean velocity errors of 0.14 and 1.98 cm.s-1 for U and V, respectively. The results of the hydrodynamic model will be used to drive the water quality model for bacteriological dispersion and decay, aiming to predict its potential influence on local bivalve farms.