Chlortetracycline (CTC), an antimicrobial administered as a feed additive to cattle, swine, and poultry, is present in the corresponding manure. Land application of raw or processed (composted or stockpiled) manure provides a mechanism by which CTC (and other antimicrobials) enters the environment and becomes available for transport to surface receiving waters via rainfall or snowmelt runoff. Chlortetracycline has been detected in Canadian surface waters, but little has been reported on its fate in aquatic ecosystems. To address this knowledge gap, the dissipation of CTC-enol was monitored in deionized water and water typical of wetlands within the prairie region of Canada. In deionized water, CTC-enol tautomerized to CTC-keto, and both tautomers epimerized to 4-epi-CTC-enol and 4-epi-CTC-keto, respectively. Irreversible isomerization to iso-CTC occurred, which then epimerized to 4-epi-iso-CTC. In wetland water, although tauterization of CTC-enol to CTC-keto occurred, there was no evidence of the formation of the 4-epimers of either CTC-enol or CTC-keto. The major product formed in the wetland water was iso-CTC, some of which epimerized to 4-epi-iso-CTC. Although CTC-enol was shown to tautomerize to CTC-keto, the concentration of CTC-keto remained low in both deionized and wetland water, suggesting that the isomerization of CTC-enol to iso-CTC most likely occurred via CTC-keto. The dissipation of CTC-enol in wetland water was described by pseudo first-order kinetics with a DT50 (time required for 50% dissipation) value of 4.8 h. The short DT50 value of CTC and reduced antimicrobial activity of iso-CTC and 4-epi-iso-CTC suggest a lower probability for selection for CTC-resistant bacteria in Canadian Prairie aquatic ecosystems.