In response to the growing recognition of the potential effects of near-bed hydrodynamics on various benthic processes, flume studies were conducted to document fine-scale flow patterns over several types of mudboxes that have been used to study colonization by deep-sea organisms. Mudboxes are typically filled with natural sediments or sediment treatments and placed in the field to observe how timing, larval supply and sediment composition may affect larval settlement. This study addresses potential hydrodynamic biases of mudbox structures as obstructions to the near-bed flow. Detailed velocity profiles were made over two types of “free vehicle” mudboxes that could be deployed and recovered from a surface vessel. One of these (“Old Free Vehicle”) was not designed with regard for potential hydrodynamic biases whereas the other (“New Free Vehicle”) was designed specifically to minimize flow disturbances and maintain a realistic boundary-layer flow over the mudbox sediments. Flume velocity profiles also were made over two smaller mudboxes designed to be deployed by a submersible, one (“Flush Sediment Tray”) which was designed to be placed flush with the ocean bottom, thus minimizing flow disturbance, and another (“Raised Mudbox”) which was not. Flume simulations indicated that the Old Free Vehicle and the Raised Mudbox cause considerable disturbance to the near-bed flow regime; flows over the mudbox sediment surface differed markedly from those predicted for the natural seabed and those observed over the flume bed in the absence of the mudboxes. Flow accelerations, growing secondary boundary layers and eddy formation were observed over these mudbox sediments, and vertical velocity profiles varied considerably in the along-channel direction. The alternative mudbox designs (New Free Vehicle and Flush Sediment Tray) were largely successful in reducing or eliminating these flow artifacts. Boundary-layer flows over both the New Free Vehicle and the Flush Sediment Tray were much more uniform, and velocity profiles over the sediment surfaces were very similar to those in the empty flume channel and those predicted for a natural deep-sea habitat. In addition, there was no evidence of eddy formation and other major flow disturbances. These flume studies underscore the benefit of considering potential hydrodynamic effects in designing benthic experimental sampling gear to reduce potential flow disturbances that may bias data collections and confound data interpretation.