Ecological damage by scuba divers has been extensively studied in marine ecosystems, particularly coral reefs, whereas the impacts on freshwater environments such as groundwater springs is unknown. In the Silfra groundwater fissure in Iceland, a vast increase in diver entries has occurred during the last decade, prompting concerns over potential ecosystem impacts and visitor carrying capacity. Here, a mixed-method approach was used to assess the impacts of scuba diving in Silfra. (a) Divers were recorded under water to observe the mechanisms of diver-related disturbances, (b) benthic material was collected along transects in Silfra and the undisturbed fissure Flosagjá to compare biofilm biomass and zoobenthic communities between and within fissures, and (c) the perceptions and experiences of stakeholders surrounding the dive tourism in Silfra were explored. Underwater observations showed that 91.4% of the divers caused at least a single disturbance, resulting in biofilm detachments and/or sediment stirring. Diver fins caused the most frequent disturbances, predominantly through fin-generated currents but also by directly contacting the substrate. Benthic biofilm biomass was lower in Silfra than Flosagjá and exhibited a negative correlation with dive-use. Some disturbance-tolerant zoobenthic groups exhibited moderate to strong correlations with dive-use. All stakeholders had negative perceptions towards increasing diver entries, but although entry limitation could improve tourism quality, disturbance might only minimally be reduced as springs like Silfra may be particularly sensitive. Springs are characteristically stable and uniform environments that can be vulnerable to disturbance. Their use for scuba diving should be carefully managed through a holistic approach and an active collaboration between all stakeholders.