In-water shark-based tourism is growing worldwide and whale sharks (Rhincodon typus) are one of the most popular targets of this industry. It is important to monitor tourism industries to minimize any potential impacts on target species. At Ningaloo, Western Australia, Electronic Monitoring Systems (EMS) have been installed on licensed tour vessels to collect information on encounters between snorkelers and whale sharks. This study combined data from the EMS with whale shark identification photographs, to assess the impact of in-water tourism on the encounter duration for individual sharks. During 2011 and 2012, 948 encounters with 229 individual sharks were recorded using EMS. Encounter durations between whale sharks and tourism vessels ranged between 1 and 59 min (mean = 11 min 42 s, SD = ±11 min 19 s). We found no evidence for a decline in encounter duration after repeated tourist encounters with individual sharks. Encounter duration varied among tourism operator vessels and were shorter when the sex of the whale shark could not be identified. Given that individual sharks were swum with on average 2.4 times per day (±SD 2.08), and up to 16 times over the course of the study, our results suggest that there is no evidence of long-term impacts of tourism on the whale sharks at Ningaloo. However, the inclusion of well-defined categories of whale shark behaviors and information regarding how interactions between tourists and whale sharks end will complement the data already collected by the EMS. This preliminary investigation demonstrates the potential for the EMS as a data resource to better understand and monitor the impacts of tourism interactions on whale sharks.