The inclusion of unpurified plant ingredients can increase particle size, improve particle recovery with microscreens and hamper COD short-term biodegradability in feces of rainbow trout. Ultrasound treatment had only very limited effects on the particle size distribution in feces, the particles forming the fecal pellet showed to be very resilient to mechanical stress. Although ultrasound treatment increased carbon bioavailability by 7–10%, we conclude that ultrasound is not a feasible conditioning method to increase carbon bioavailability for denitrification in RAS.