We numerically estimated the inflow flux of terrestrial grass, which is the main floating macro-debris, into Tokyo Bay from April 2008 to March 2009 based on a two-way particle-tracking model and an inverse method applying a Lagrange multiplier. In the estimation, we used surface current velocities derived by high-frequency ocean radar and the quantity of grass collected by clean-up vessels which are operated daily in the bay. At least 2115 m 3 yr −1 of the grass flowed into the bay annually, and the contribution of a flood event to the inflow flux of grass was larger than that of the inflow flux of freshwater. We show that 39% of the annual inflow flux of grass into the bay was collected, and 61% flowed out of the bay or sank to the seabed. The numerical estimation in this study will be useful to establish a system for predicting patches of floating macro-debris in the bay, and to evaluate the effects of river development or clean-up along river banks and flood plains in the upper reaches.