Short chain chlorinated paraffins (SCCPs) are a group of complex emerging persistent organic pollutants. In this study, the uptake, translocation, and transformation of four constitutionally defined SCCP isomers were studied using whole pumpkin ( Cucurbita maxima × C. moschata) and soybean ( Glycine max L. Merrill) seedlings via hydroponic exposure. Results showed that the daughter SCCPs were C10Cl5-8 and C11-13Cl5-6. The metabolic transformation of all tested isomers included dechlorination and chlorine rearrangement. In addition, carbon chain decomposition products were found for isomers with trichlorinated carbon atoms (CCl3-groups) in both pumpkin and soybean seedlings. This study provides the first evidence of carbon chain decomposition of SCCPs in whole plants, and it suggests new metabolism pathways of SCCPs in the environment. The influence of carbon chain length and degree of chlorination of SCCPs on their fate and behavior within different plant species were also investigated. Bioaccumulation of SCCPs in pumpkin and soybean increased with increasing carbon chain length and degree of chlorination. In comparison, soybean translocated and degraded parent SCCPs faster and to a greater extent than pumpkin, but pumpkin accumulated parent SCCPs to a greater extent than soybean. After 10 days exposure, less than 4% of the initial mass of exposed chemicals remained in solution of exposure groups. The parent chemicals accumulated in roots ranging from 23.6% to 59.9% for pumpkin and 1.98% to 54.5% for soybean and in stems ranging from 0.7% to 3.81% for pumpkin and 0.50% to 2.54% for soybean. These results give new perspectives on the transport, transformation, and fate of SCCPs in the environment.