Between January 29 and February 11, 2019, the Townsville region in Australia experienced a major flooding event. This study explored impacts on affected community pharmacies. Semi-structured phone interviews were conducted with six pharmacists who worked in affected Townsville community pharmacies during this flood. De-identified transcript data were analyzed using reflexive thematic analysis. The thematic analysis yielded six themes – “financial impact on pharmacy owners,” “engagement with Local Disaster Coordination Center (LDCC) important,” “workload pressures,” “preparedness,” “medication supply impacts,” and “communication and collaboration.” Financial impacts to owners included loss of property (two pharmacies were completely flooded), purchase or hire costs of generators when power was lost, and loss of revenue from complete or early closure of pharmacies and when patients could not pay or did not have a prescription and did not return to the pharmacy after the event. Engagement with the LDCC assisted pharmacy responsiveness. Medication supply issues were experienced by patients whose houses had flooded, or who had left their prescriptions with pharmacies that had flooded. Opioid Replacement Therapy (ORT) program patients were also impacted due to communication difficulties between them, their clinics, and their pharmacies. Increased customer numbers by those whose regular pharmacy was closed, reduced staff numbers, and austere working conditions increased workload pressures. Pharmacists collaborated to consolidate resources with those whose pharmacy had closed, working in pharmacies that were open. This research highlights a critical need for improved flood preparedness among Townsville pharmacists. Regardless, they collaborated to ensure there were minimal critical medication delays.