Detritus is an important energy source of stream food webs. Being a mix of allochthonous and autochthonous sources, it is often unknown, which components contribute to the growth of stream organisms. This study focussed on the comparison of two different detritus types (riparian detritus and stream detritus) with respect to food quality and effects on growth as a fitness parameter of juvenile freshwater pearl mussels (FPM). We performed feeding experiments with juvenile FPM under laboratory conditions using the two detritus types from four different natural sources each. Food quality was determined by analysing the fatty acid composition. Stream detritus (conditioned to stream environment including autochthonous microbes) resulted in significantly higher growth rates of juvenile FPM than predominately terrestrial-based riparian detritus indicating higher food quality. Significantly positive correlations were found between mussel growth and different groups of polyunsaturated fatty acids (PUFA). This suggests that especially trace substances such as long-chained n-3 PUFAs and a high ratio of n-3 to n-6 PUFAs enhance the food quality of stream detritus for juvenile FPM. These results highlight the importance of instream conditioning of detritus for the food mix in headwater streams and the importance of PUFAs for the development of juvenile FPM.