We discuss modeling of the transport and deceasing of Escherichia coli in the sea. From the measured and extrapolated data on salinity and water temperature, and the data on average daily solar radiation and water turbidity, the coefficient of E. coli deceasing rate was calculated according to Mancini's equation for each cell of the domain in the part of the Koper Bay. With the modified Nafta3D model, using the precomputed hydrodynamics and different particle (bacteria) properties we performed a forty-eight hour simulation of an instantaneous and a continuous release of particles from a single source, and analyzed locations of two particle types: free E. coli (ECF) and E. coli bound to suspended solids (ECA). Then we analyzed the ECA and ECF activity with the newly developed E. coli decease model at both discharge types using a first order kinetics equation (Chick's law). Bacteriae activity gradually decreased due to environmental factors attributed to each cell of the computational domain by the decease coefficient rate. Within forty-eight hours the ECA sank close to the bottom and mostly stayed within the second basin of the Port of Koper. The decease-time of 90% of the ECA(T90) for continuous discharge was found to be over 48 hours, and about 48 hours for the instantaneous release. The ECF were moving farther from the source and partly left the second basin. ECF hover higher in the water column; therefore, due to the environmental factors, we found the T90 to be 6 and 10 hours at at an instantaneous and a continuous discharge, respectively.