The red-knobbed coot Fulica cristata experienced a dramatic population decline in Spain, where the common coot F. atra does not face conservation problems. This is puzzling because both species have similar ecologies. It has been suggested that habitat alterations affected the quality of food plants, and this impacted differentially both coots. To verify this, we conducted experiments to determine the assimilation efficiency of both species in relation to food quality. Two types of diets differing in fibre content (commercial food and Potamogeton pectinatus) were offered to captive red-knobbed and common coots, during both spring and autumn. We examined variations in faecal particle size among coot species and diets, indicative of the facility with which food can be assimilated, and used the stable isotope technique to study differences between coot species in stable isotope fractionations from consumption to excretion. Faecal particle size was larger in red-knobbed than in common coots when fibre content was high, but was similar when it was low. Faecal particle sizes were larger in autumn, when fibre content was higher, than in spring. In general, delta(15)N in faeces of red-knobbed coots was greater than in faeces of common coots. These results suggest that the digestive efficiency of the red-knobbed coot was lower than that of the common coot, and that the differences increased when the fibre content in food plants increased. Managers should try to make available to coots wetland habitat with high quality food, which may be facilitated by prolonging the hydroperiods.