INTRODUCTION: Skin and soft tissue infections have the potential to affect every patient admitted to a surgical service. Changes to the microbiota colonizing wounds during natural disasters, such as the Townsville floods of 2019, could impact empiric antibiotic choice and need for return to theatre. METHODS: This retrospective observational cohort study reviews culture data and demographics for patients undergoing surgical debridement of infected wounds over a six-month period starting in November 2018 to May 2019 at the Townsville Hospital. RESULTS: Of the 408 patients requiring operative intervention, only 61 patients met the inclusion criteria. The groups were comparative in terms of age and gender, but a greater proportion of patients (40.5% versus 29.1%, P = 0.368) in the post-flood group were diabetic. Common skin commensals, such as Staphylococcus aureus, were the most common pathogen in both groups, however the post-flood group had a higher proportion of atypical organisms (14 versus 8 patients), and an increased need for repeated debridement for infection control (24 versus 14 patients). CONCLUSION: Wound swabs and tissue culture are imperative during surgical debridement and may guide the use of more broad-spectrum coverage following a significant flooding event.