To reveal the influence of shape factors on the effective density (ρe) of cohesive sediment, a series of laboratory experiments has been conducted under different turbulence intensities using a submersible digital holographic camera (LISST-Holo). Shape factors representing axis ratio, boundary roughness, and sturdiness of flocs exhibited characteristic variations with turbulence intensity. For turbulence intensities from 0.54 to 1.42 Pa, micro-flocs were broken into single grains, resulting in a constant axis ratio, a 13% decrease in boundary roughness, and a 16% increase in sturdiness. Out of these shape factors, ρe was mainly derived from the concept of sturdiness, which represents the fraction of primary particles within flocs. In fact, the 16% increase in sturdiness added 9% to ρe. When the flocs became sturdier, ρe had lower dependence on floc size due to the increase in the fraction of primary particles. Furthermore, ρe as a function of floc size might be affected by the response of the optical instrument. In the case of fine particles (<25 μm), not every suspended particle was reconstructed from the holographic image, inducing an underestimation of ρe. This is because insufficient scattering from floc edges impacts the particle detection ability. Despite the uncertainties, LISST-Holo is well suited to obtain a series of data for shape factors of flocs. These outcomes give insight into means for estimating ρe.