Abundance and biochemical composition of organic materials in sediments of the estuaries of Mundaka and Bilbao (SE Bay of Biscay) were analysed to assess the effect of organic wastes released to these systems. Organic and labile contents were higher in the sediments of Bilbao, denoting organic enrichment with poorly decomposed materials by human dumping. Spatially, organic matter distribution skewed seaward in Bilbao and upward in Mundaka, in agreement with the location of major point sources of sewage. Labile material, proteins and protein:carbohydrate ratio showed upward increases in both estuaries, attributed to the oxygen restrictive conditions to decompose organic materials. Vertical distribution of organic components into sediments reflected the history of human activities. In Bilbao, the significant reduction of organic and labile compounds, and the decrease of protein:carbohydrate values in top layers seem a result of recent remedial actions to reduce urban sewage inputs and improve environmental conditions. Higher contributions of proteins and lipids were associated with anthropogenic materials, and higher contributions of carbohydrates with autochthonous materials. High protein:carbohydrate values indicate poorly decomposed materials of human origin. The close relationship of carbohydrates with chloropigments in Mundaka suggests that phytobenthic populations and derived detritus contributed to a greater extent to the organic fraction in this estuary.