A one-dimensional numerical model describing tidally varying vertical mixing and settling was used to interpret sediment concentrations and vertical fluxes observed in the shoals of South San Francisco Bay by two acoustic Doppler velocimeters (ADVs) at elevations of 0.36 m and 0.72 m above bed. Measured sediment concentrations changed by up to 100 g m⁻³ over the semidiurnal tidal cycle. These dynamics were dominated by local resuspension and settling. Multiple particle class models suggested the existence of a class with fast settling velocities (w_s of 9.0 × 10⁻⁴ m s⁻¹ in spring and 5.8 × 10⁻⁴ m s⁻¹ in fall) and a slowly settling particle fraction (w_s of <1 × 10⁻⁷ m s⁻¹ in spring and 1.4 × 10⁻⁵ m s⁻¹ in fall). Modeled concentrations of slowly settling particles at 0.36 m were as high as 20 g m⁻³ during fall and varied with the spring-neap cycle while fine sediment concentrations in spring were constant around 5 g m⁻³. Analysis of in situ water column floc size distributions suggested that floc properties in the lower part of the water column were most likely governed by particle-size distribution on the bed and not by coagulation, validating our multiple particle size approach. A comparison of different sediment bed models with respect to model performance, sensitivity, and identifiability suggested that the use of a sediment erosion model linear in bottom shear stress τ_b (E = M (τ_b − τ_c)) was the most appropriate choice to describe the field observations when the critical shear stress τ_c and the proportionality factor M were kept constant.