There is a growing trend towards culturing fish in intensive recirculating aquaculture systems, which have a reduced need for water exchange compared to many other systems. However, it is unknown whether these intensive aquaculture operations facilitate bioaccumulation of trace elements in fish tissue. The present study therefore evaluated and compared the accumulation of 20 trace elements in the flesh of marbled eel Anguilla marmorata reared in 3 different systems: a recirculating aquaculture system (RAS), a biofloc technology system (BFT), and a concrete pond (CP; traditional method). In the BFT system fish were also raised in polyculture with tilapia Oreochromis niloticus and water spinach Ipomoea aquatica Forsk. Fish were fed the same feed and reared in water from the same source. The trace elements (Al, As, Ba, Be, Co, Cr, Cu, Fe, Li, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, Ti, V, and Zn) in the fish flesh were analyzed by inductively coupled plasma-optical emission spectrometry. Fish reared in the RAS had elevated concentrations of only a single element (Al) compared with CP fish. This element was also elevated in BFT fish and was probably related to the high Al concentration in the fish feed. Fish reared in the BFT system also showed significantly higher levels of As, Ba, Cr, Fe, Mn, Ni, Se, Sn, Sr, Ti, and Zn compared to both CP and RAS fish. The observed levels of (1) As in fish from BFT systems and (2) Pb in fish from both RAS and BFT systems exceeded national and international legislatory limits. Our results suggest that regular monitoring of trace element concentrations in BFT and RAS should be implemented in the future for this species.