Detection of SWCNTs in complex matrices presents a unique challenge as common techniques lack spatial resolution and specificity. Near infrared fluorescence (NIRF) has emerged as a valuable tool for detecting and quantifying SWCNTs in environmental samples by exploiting their innate fluorescent properties. The objective of this study was to optimize NIRF-based imaging and quantitation methods for tracking and quantifying SWCNTs in an aquatic vertebrate model in conjunction with assessing toxicological end points. Fathead minnows (Pimephales promelas) were exposed by single gavage to SWCNTs and their distribution was tracked using a custom NIRF imaging system for 7 days. No overt toxicity was observed in any of the SWCNT treated fish; however, histopathology observations from gastrointestinal (GI) tissue revealed edema within the submucosa and altered mucous cell morphology. NIRF images showed strong SWCNT-derived fluorescence signals in whole fish and excised intestinal tissues. Fluorescence was not detected in other tissues examined, indicating that no appreciable intestinal absorption occurred. SWCNTs were quantified in intestinal tissues using a NIRF spectroscopic method revealing values that were consistent with the pattern of fluorescence observed with NIRF imaging. Results of this work demonstrate the utility of NIRF imaging as a valuable tool for examining uptake and distribution of SWCNTs in aquatic vertebrates.