We present results from an on-going research effort which aims at applying the Smoothed Particle Hydrodynamics (SPH) method to the large-scale particle transport as well as complex flows involving particle-suspension/structure interaction. The main application to this modelling work is related to the estimation of the seabed disturbance created by a moving harvesting device near the seabed for deep-sea applications. Current results are presented for a lab-scale model of sediment disturbance in the vicinity of the harvester as well as ocean-scale sediment transport. The latter includes new developments on SPH formulations of anisotropic diffusion.