Clogging of the submerged entry nozzle (SEN) in continuous casting of steel occurs due to the solid material build-up on the inner wall of the SEN. Different mechanisms have been proposed for clogging but attachment of solid non-metallic inclusions (NMIs) is supposed to be the dominant mechanism. In this work, effects of clogging on the melt flow and non-metallic inclusions (NMIs) distribution in the mold region were investigated transiently using a numerical model. In this model, inclusions are considered as solid spherical particles and their motion is calculated in a Lagrangian frame of reference; the turbulent melt flow is simulated with an Eulerian approach. NMIs attach on the inner wall of SEN due to the turbulent melt flow to form clog material and the clog growth changes the melt flow field simultaneously. With two-way coupling between clog growth and melt flow, transient behavior of the melt flow in the mold region can be investigated. The simulation results showed an asymmetric flow pattern and consequently an asymmetric inclusion and temperature distribution in the mold region. Effects of transient clogging on dynamic flow direction on the meniscus were also addressed. Using this numerical model, the effects of clogging on the different parts during the casting process can be predicted.