The metabolism of organism, defined as an assortment of complex chemical processes that the organism is capable of performing. Metabolic rate depends on biotic and abiotic factors that can usually be determined indirectly by measuring oxygen consumption rate in a given period of time in aquatic animals. Due to the increasing presence of metal contaminants in aquatic ecosystems, many studies have been carried out about the effects of heavy metals on fish metabolic rate. Measurement of the rate of oxygen consumption along with metabolites excreted by fish can be useful tools in understanding the effects of stresses caused by heavy metals in fish. Hence, at the present study the effects of water-borne copper and lead on metabolism (standard metabolism, maximum metabolism and aerobic scope) and metabolites excretion by bahaii loach ( Turcinoemacheilus bahaii ) were investigated. To address this, 170 fish were collected from Zayandeh Roud River at Khersunak locality in Chaharmahal and Bakhtiari province. After acclimation of fish to the laboratory condition for three weeks, the median lethal concentration (LC 50 -96h) for copper and lead were determined. According to the LC 50 -96h results, 72 fish (average weight 1.2 ± 0.56 g and average length 6.2 ± 0.97 cm) were divided into 9 different treatments group, including control, copper’s (24h, 0.910 mg/l), (7d, 0.455 mg/l), (14d, 0.182 mg/L) and (30d, 0.091 mg/l) as well as lead’ (24h, 124.430 mg/l), (7d, 62.215 mg/l), (14d, 12.443 mg/l) and (30d, 6.221 mg/l). Eight fish were assigned to each treatment and each fish was considered as replicate. Intermittent-flow-respirometer was used to measure the metabolic rate of bahaii loch. Metabolites of fish (ammonia excretion) were measured by using the colorimetric method. Histopathological examination of gills and kidney of fish was carried out by H E staining. Results showed significant (P 0.05) reduction in standard metabolic rate (SMR) of fish exposed to copper and lead. The minimum SMR related to copper-treated fish for 30days (43.90 ± 14.86 mgO 2 /kg/h) was reduced by about 70%, as compared to the control group (148.10 ± 12.73 mgO 2 /kg/h). Although the maximum metabolic rate (MMR)and the aerobic scope in the copper-treated fish showed no significant differences with the control groups, but the lead-treated fish showed significant differences (P 0.05). Maximum amount of aerobic scope was observed in a group treated by lead for 30days, being1.7 fold of the control group. Regarding the excreted metabolites, results showed that the ammonia excretions were reduced significantly (P 0.05) in both copper and lead treated fish. The minimum ammonia excretion rate (10.5 ± 1.81 mg/kg/h) was observed in copper treated fish (30d, 6.221 mg/l), which is reduced by 84.61% in comparison with control group. Exposures to either metal led to histopathological damages in gills such as hyperplasia and fusion of secondary lamellae, clubbing and detachment of epithelial lamella. Histopathological damages in kidney such as necrosis, atrophy, dilation and etc. of the renal tubules were also observed. According to the results, it appears that lead and copper could disrupt metabolism and excreted metabolites of fish due to gills and kidney tissue damages. Keywords: Metabolism, Metabolites excreted, Heavy metals, Turcinoemacheilus bahaii