The influence of aggregation on cohesive sediment erosion and settling was investigated in a semi-enclosed coastal lagoon with a bed consisting of sediment in the clay to sand size range. Cores of bed material and seawater were used for ex situ laboratory experiments investigating the erosion of the sediment bed and the settling of aggregates. The results showed that the cohesive bed was primarily eroded as aggregates and aggregation was the major contributor to the formation of microflocs in the system. The aggregates eroded from the bed were relatively stable up to a bed shear stress level of at least 0.5Nm−2. The eroded aggregates displayed high settling velocities relative to the aggregate sizes in comparison to previous water column studies from similar environments. Since high settling velocities limit the advective transport, the erosion of aggregates potentially plays a significant role for the cohesive sediment dynamics of a coastal system. The impact of aggregation on cohesive sediment erosion and settling is important to understand in order to improve general understanding of coastal environments and to strengthen the reproduction of cohesive sediment dynamics in numerical models.