Microphytobenthic polymers mediate intertidal sediment erosion processes, through biostabilization and modifying the nature of eroded floc material. The latter is of key importance with respect to sediment transport dynamics, including floc aggregation and particle deposition. In this study, eroded floc material was analyzed by video imaging, alongside novel application of in-line laser holography (ILH). The erosion of engineered sediment was compared to that of natural estuarine sediments. Both video and holography showed an increase in floc size eroded from engineered cohesive clay sediment as a function of sediment dewatering and sediment polymer content. Estuarine sediment showed a curvilinear increase in floc size as a function of both microphytobenthic biomass and sediment colloidal polymer content when measured by video analysis. Holography did not show these functions for floc size due to temporal limitations of the current ILH methodology. An interaction of sediment polymer binding and sediment desiccation was observed for engineered sediments and, most notably, for estuarine cohesive sediments. In conclusion, engineered sediments were not accurate analogues for natural intertidal sediments, failing to reproduce eroded floc material similar to that from estuarine cohesive sediment. The size of eroded floc from estuarine sediments is a function of the complex interaction between biological and physicochemical processes, primarily algal colloidal polymer and desiccation. Holography demonstrated an excellent potential for the high-resolution imaging of eroded material but is limited by temporal constraints; the solution to this would be the development of real-time holographic video.