This work introduces the Locally Filtered Transport (LFT) method for numerical transport models. Locally turning off the transport computation in areas of nearly uniform concentration is proposed as a new approach for reducing computational cost in ecosystem models that require transport of tens to hundreds of constituent concentrations. The proposed method is locally mass conservative just as the discontinuous Galerkin finite element scheme it is based on. The performance of the method is illustrated using numerical examples including an advection-reaction ecosystem simulation with a simple nitrogen, phytoplankton, and zooplankton (NPZ) model.