A two-dimensional, vertically integrated, non-linear numerical model was applied to investigate the Urias coastal lagoon’s (URCOL) tide-driven currents, bed load sediment transport, and seabed morphodynamics. The coastal body of water, located on the eastern side of the Gulf of California, includes the Mazatlán harbour, the most important port on the Pacific Mexican coast due to the relevant activities like the heavy vessel traffic. URCOL also includes an extensive aquaculture infrastructure at the lagoon head. The tidal hydrodynamic modelling revealed the mixed character of tides predominantly semidiurnal in the lagoon. The numerical computation at the harbour entrance showed an ebb-dominant tidal distortion. The distribution patterns of the erosion and accretion rates are consistent with the convergent and divergent character of the vectors of sediment transport rates. The sediment accretion has been predicted mainly in the middle part of the channel, right where the channel starts curving, changing the alignment of the lagoon. The tidal hydrodynamics, sharp topographic gradient, and geometric features of the lagoon seem to determine the location of accretion and erosion areas.