In-situ sampling, characterization and quantification of colloidal aggregates and flocs in ambient water is complex but needed in order to understand their role in development and maintenance of moving fluid muds, muck, bottom boundary lutocline layers and nephelometric interfaces in aquatic systems. These bottom boundary interfaces and associated processes contribute to sedimentation, particle deposition and resuspension of total particulate matter and associated nutrients. Increasing the scientific understanding of the above requires advances in environmental sensing instrumentation (passive and active) to successfully understand these aquatic interfaces. Standalone in-situ sensors that automatically perform multiple steps including sampling, separation, and detection have the potential to greatly advance analytical science. A new in-situ multispectral optical camera system for environmental monitoring and surveillance of delicate flocs and related aggregate structures is described. Results of the system show that flocs - 0.1 mm –10.2 mm diameter (mean diameter of 2.77 mm), with a variance of 5.952 mm and a median effective cross-section area of 30 mm2 can be measured using the passive multispectral optical imaging system. The system is lightweight, compact and suitable for shallow or deep water deployment. When combined with fixed station acoustic echogram instruments, nephelometric (turbidity) waves can be easily observed. Time sequential analysis of imagery allows the system to be used as an optical particle velocimetry system (OPVS). Initial shallow water testing resulted in Lagrangian particle velocities of 0.3 to 3 cm sec-1 to be measured. Similar results were obtained from an acoustic velocity current meter (MAVS3) and a Marsh McBirney 201D electromagnetic current meters. When combined with results from direct methods using sondes for estimating sediment mass fluxes, the combined systems provide data necessary for sediment and water quality modeling. The new optical sensor system will help address analytical needs reported in past studies and provides a new standard method and protocol for measuring the movement of sediment and particulates in the aquatic bottom boundary layers.