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Abstract Estuarine and coastal regions are often characterized by a high variability of suspended sediment concentrations in their waters, which influences dredging projects, contaminant transport, aquaculture and fisheries. Although various three-dimensional open source software are available to model the hydrodynamics of coastal water with a sediment module, the prediction of the fate and transport of cohesive sediments is still far from satisfied due to the lack of an efficient and robust flocculation model to estimate the floc settling velocity and the deposition rate. Single-class and sometimes two-class flocculation models are oversimplified and fail to examine complicated floc size distributions, while quadrature-based or multi-class based flocculation models may be too complicated to be coupled with large scale estuarine or ocean models. Therefore, a three-class population balance model was developed to track the sizes and number concentrations of microflocs, macroflocs and megaflocs, respectively. With the assumption of a fixed size of microflocs and megaflocs, only four tracers are needed when coupled with the open-source TELEMAC system. It enables better settling flux estimates and better addresses the occurrence and concentration of larger megaflocs. This tri-modal flocculation model was validated with two experimental data sets: (1) 1-D settling column tests with the Ems mud and (2) in-situ measurements at the WZ Buoy station on the Belgian coast. Results show that the flocculation properties of cohesive sediments can be reasonably simulated in both environments. It is also found that the number of macroflocs created, when a larger macrofloc breaks up, is a statistical mean value and may not be an integer when applying the model in the field. Graphical abstract Image Highlights • The sizes of flocs are dynamically altered because of particle aggregation and breakage. • A three-class population balance flocculation model was developed. • This flocculation model has been successfully implemented in the open source TELEMAC. • Four tracer variables, representing the floc size distributions, were included in TELEMAC. • The model was validated with settling column tests and field measurements. [ABSTRACT FROM AUTHOR]