The generation of organic waste associated with aquaculture fish processing has increased significantly in recent decades. The objective of this study is to evaluate the anaerobic biodegradability of several fish processing fractions, as well as water treatment sludge, for tilapia and sturgeon species cultured in recirculated aquaculture systems. After substrate characterization, the ultimate biodegradability and the hydrolytic rate were estimated by fitting a first-order kinetic model with the biogas production profiles. In general, the first-order model was able to reproduce the biogas profiles properly with a high correlation coefficient. In the case of tilapia, the skin/fin, viscera, head and flesh presented a high level of biodegradability, above 310 mLCH4 gCOD−1, whereas the head and bones showed a low hydrolytic rate. For sturgeon, the results for all fractions were quite similar in terms of both parameters, although viscera presented the lowest values. Both the substrate characterization and the kinetic analysis of the anaerobic degradation may be used as design criteria for implementing anaerobic digestion in a recirculating aquaculture system.