The function of a gravel-bed wetland in treating wastewaters is dependent on the turn-over rate of organic matter (OM) fractions in accumulated solids. Organic deposits from a gravel-bed planted (Schoenoplectus tabernaemontani) wetland, which had experienced pore clogging after 5 years of receiving farm dairy wastewater were therefore collected and determined for labile (water-soluble) and stable (humic acid, fulvic acid and humin) OM fractions, total carbon (C), microbial biomass and microbial respiration rate. Over 90% of the accumulated organic solids was present as stable fractions, with humic compounds at least 2-fold higher in surface deposits and the top 100mm of the gravel bed than the lower gravel substratum. Clogging of the gravel pore spaces over a 5-year wetland operation was probably due to the accumulation of refractory (stable) organic solids, particularly in the top 100 mm of the gravel bed. Microbial respiration rate and microbial biomass were significantly correlated with stable OM fractions, suggesting that these microbial parameters may be used to predict the nature of accumulated OM fractions. Further research is required to evaluate the use of these parameters as indicators of labile and stable fractions in wetlands with a range of OM loadings and accumulation.