To gain insight into the microscopic processes leading to the observed collective settling of particles from the base of a particle-bearing fresh water layer overlying salt water, we perform numerical simulations of the settling of weakly inertial particles through uniform density, uniformly stratified and nonuniformly stratified fluids. Intuition is gained first through simulations of a descending horizontal row and planar arrays of particles. These show that stratification acts to reduce cluster sizes and to slow the relative descent speed of clusters as a result of upward flows that develop around the clusters. This occurs even for a descending vertical planar array: in unstratified fluid, the ambient fluid rises laterally around the particles with the flow in the plane of the particles being predominantly downward; in stratified fluid, upward as well as downward motion is evident in the plane of particles. For a random three-dimensional particle array with concentration by volume between 0.1% and 1%, upflows in the ambient fluid likewise retard cluster formation and descent speeds. The mean horizontal displacement of the particles is reduced, resulting in more small clusters with more closely packed particles. The particles become more verti- cally aligned in lower diffusivity (higher Schmidt number) fluid, although such clustering takes longer to develop. The results suggest that both stratification and relative diffusivity play a crucial role in the collective settling behavior observed in laboratory experiments.