Forced swimming in cold water causes physiological and psychological stress that leads to altered biochemical homeostasis and neurobehavioral responses. In this study, plasma and urinary metabolites in Sprague-Dawley (SD) rats subjected to cold water forced swimming stress (CWFSS) were characterized using NMR in conjunction with multivariate data analysis. Metabolic analysis demonstrated that decreased levels of lipoprotein and increased levels of O-acetyl glycoprotein, glucose, lactate, pyruvate, creatine, citrate, succinate and amino acids including phenylalanine, tyrosine, glutamate, valine, isoleucine, alanine and lysine in plasma were observed in response to CWFSS. Moreover, the biochemical response to CWFSS as determined from NMR analysis of urine was characterized by an elevation of gut microbiota-related metabolites including phenylacetylglycine, 4-cresol glucuronide and indoxyl sulfate. These results suggest that CWFSS-induced metabolic perturbations were involved in the disruption of amino acid and energy metabolism as well as the alteration of gut microbiota function. This study will enhance the current knowledge of stress-induced diseases and aid in the early diagnosis of metabolic disorders in humans.