A portable erosion flume has been developed that is capable of estimating erosion threshold and erosion rate relationships for fine-grained specimens over the depth of a typical sample tube. This newly-designed apparatus is a recirculating flume capable of generating steady currents over the exposed section of the sample. In this paper, the erosion properties of two marine sediments have been determined and show a significant systematic variation with depth at centimetre scale that would have implications for the potential need for scour protection engineering. The tests showed that the critical erosion onset velocity doubled over the upper 200 mm of each sample, and the erosion rate fell by an order of magnitude. The increased erosion resistance with depth is consistent with the general trend of erodibility reducing with decreasing moisture content. Ignoring this depth effect when selecting design values of the erosion properties could lead to erroneous predictions of scour rate and extent around subsea structures, and unnecessary scour protection engineering costs.