The very early diagenesis of particulate organic matter, particularly that of carbohydrates and amino acids, was studied in the course of the transportation of particulate organic matter through the water column with sediment traps in Lake Haruna. There was a great difference in neutral sugar and amino acid composition ratio between suspended particles and sinking particles. However, there was a similarity in the composition ratio between sinking particles and surface sediment. The results on neutral sugar and amino acid composition ratio suggest that carbohydrates and amino acids in sinking particles were the residual fractions of particulate organic matter which had been degraded. Particulate carbohydrates and amino acids are considered to be rapidly subject to degradation process in the water column and sediment traps. The remaining refractory fractions may be slowly degraded in the sediment.