This work investigates the composition and the fate of sugars, lipids, proteins, amino acids under aerobic conditions for 13 domestic and 4 agro-industrial wastewaters, sampled before and after treatment. The rates of aerobic degradation were moreover studied with a 21-day continuous aeration batch test. It is shown that the sum of the biochemical forms represented 50 to 85% of the total chemical oxygen demand (COD). Lipids represented the half of the identified COD; sugars and proteins correspond to a quarter of the identified COD. Aerobic processes provided an increase of the relative fractions for proteins, whereas the ones of lipids decreased and sugars fraction remains stable. For the wastewaters released from cheese dairy (lipid-rich) and slaughterhouses (protein/lipid-rich), the dissolved phase after biological treatment is composed of proteins whereas the particulate one is composed of lipids. After the 21-day test, the concentration in proteins was nearby 10 mg/L. The results should be used for operations of WWTP to detect when a dysfunction is about to occur. They can be used to predict the concentrations in the treated water when upgrading an existing municipal plant that will admit agro-industrial discharge.