Carbon nanotubes (CNTs) possess unique properties that have led to an increase in their research and usage for a wide variety of fields. This growing demand of CNTs poses a major public health risk given its unregulated release into the environment. Unfortunately there is a significant information gap on the actual quantity of CNTs in the environment due to limitation of existing detection methods. This is mainly owing to the ubiquitous carbon chemistry of CNT. In response we developed a method (CNT-capture method) that is able to structurally differentiate CNT from other interference carbon materials in an aqueous medium. The affinity between single walled nanotubes (SWNTs) and specific single stranded DNA (ssDNA) was employed to capture SWNTs in water. SWNT-specific separation was obtained via magnetic separation. Dual fluorescent labels attached to sandwich ssDNA probes were used for quantification. The specific affinity between DNA and SWNTs was verified and no significant side-interactions were observed. With optimized incubation duration (30 min) and buffer composition (10-7 % sodium dodecyl sulfate and pH 7.9), a calibration curve of quantification (R2 = 0.90) was obtained with a range of SWNT concentration (0.05-10 μg/mL) against graphene as a planar analog. Comparison to other spectroscopy based methods was carried out to highlight the specificity and sensitivity of the presented method for CNT detection in aquatic sample.