The flow of effluent through treatment wetlands is influenced by the infrastructure set-up, the effluent character, the type of hydraulic flow, the mode of operation, the type of substrate, and the type and quantity of biomass. Current flow models have not been well validated, and/or do not accurately account for biomass clogging. In this study, treatment wetlands containing Dune or River sand with similar particle size distributions exhibited significant disparities in achievable flow rates. To gain insight into this phenomenon, further investigations were conducted to compare: (i) sand particle characteristics (size, elemental and mineral composition, grain morphology), (ii) the relationships between mineral composition and shape of the sand particles, (iii) the hydraulic conductivity of the different sand types before and after inducement of biomass growth, and (iv) the measured hydraulic conductivities with those predicted using the fractional packing Kozeny-Carman model. Using automated scanning electron microscopy (QEMSCAN™) it was determined that the shape of the quartz particles of the River sand (98% quartz) and calcite particles of the Dune sand (81% quartz, 18% calcite) were less round and more angular than the quartz particles of the Dune sand, and that the River sand particles were conglomerate in nature and/or fractured. The hydraulic conductivities of the Dune and River sands were significantly different (0.284 and 0.015 mm s−1, respectively), and the hydraulic conductivity of the Dune sand decreased by 51% due to biomass accumulation. The fractional packing model overestimated the measured values.