We develop a physical and computational model for performing fully coupled, grain-resolved direct numerical simulations of cohesive sediment, based on the immersed boundary method. The model distributes the cohesive forces over a thin shell surrounding each particle, thereby allowing for the spatial and temporal resolution of the cohesive forces during particle–particle interactions. The influence of the cohesive forces is captured by a single dimensionless parameter in the form of a cohesion number, which represents the ratio of cohesive and gravitational forces acting on a particle. We test and validate the cohesive force model for binary particle interactions in the drafting–kissing–tumbling (DKT) configuration. Cohesive sediment grains can remain attached to each other during the tumbling phase following the initial collision, thereby giving rise to the formation of flocs. The DKT simulations demonstrate that cohesive particle pairs settle in a preferred orientation, with particles of very different sizes preferentially aligning themselves in the vertical direction, so that the smaller particle is drafted in the wake of the larger one. This preferred orientation of cohesive particle pairs is found to remain influential for systems of higher complexity. To this end, we perform large simulations of 1261 polydisperse settling particles starting from rest. These simulations reproduce several earlier experimental observations by other authors, such as the accelerated settling of sand and silt particles due to particle bonding, the stratification of cohesive sediment deposits, and the consolidation process of the deposit. They identify three characteristic phases of the polydisperse settling process, viz. (i) initial stir-up phase with limited flocculation, (ii) enhanced settling phase characterized by increased flocculation, and (iii) consolidation phase. The simulations demonstrate that cohesive forces accelerate the overall settling process primarily because smaller grains attach to larger ones and settle in their wakes. For the present cohesive number values, we observe that settling can be accelerated by up to 29 %. We propose physically based parametrization of classical hindered settling functions introduced by earlier authors, in order to account for cohesive forces. An investigation of the energy budget shows that, even though the work of the collision forces is much smaller than that of the hydrodynamic drag forces, it can substantially modify the relevant energy conversion processes.