The effect of bioreactor design on nitrification efficiency has been well studied, but less is known about the overall impacts on water quality. Besides nitrification, submerged fixed bed bioreactors (FBBR) trap fine solid particles, whereas moving bed bioreactors (MBBR) grind solids, possibly increasing solids and particle accumulation in the system. In this experiment, the effects of different combinations of fixed bed and moving bed bioreactors on water quality, solids removal, particle size distribution, fish health based on histopathological changes and nitrification efficiency were studied in laboratory scale recirculating aquaculture systems (RAS) with rainbow trout (Oncorhynchus mykiss). Three set-ups with triplicate tanks were used: 1. two consecutive fixed bed bioreactors (FF); 2. a fixed bed bioreactor followed by a moving bed bioreactor (FM) and 3. two consecutive moving bed bioreactors (MM). Fish performance was not influenced by the design of the bioreactor, specific growth rate (SGR) being between 1.59 and 1.64% d−1 and feed conversion ratio (FCR) between 0.95 and 0.98. Water nitrite concentration was higher in the FF systems compared to FM and MM systems, whereas the average total ammonia nitrogen concentration (TAN) was not influenced by the treatments. Nitrification rate, which was measured in the laboratory, followed the water nitrite levels, indicating highest total ammonium oxidation rates in the MM systems. UV254 absorbance and total organic carbon (TOC) concentrations were higher in the groups with moving bed systems, indicating accumulation of organic substances in the circulating water. The total volume of particles was higher in the MM systems as compared to the FF systems. The total solids balance was similar in all the bioreactor groups, since the removal of solids by the FBBR backwash was compensated by the drum filter in the FM and MM systems. In general, no significant histopathological difference in gill, kidney, heart and liver tissue were observed between the RAS treatment groups and the flow-through treatment.