Underwater noise from human activities is recognized as a world-wide problem, with important repercussions on the acoustic communication of aquatic mammals. During the COVID-19 pandemic, the government of Panama went into a nationwide lockdown to limit the spread of the virus. This lockdown resulted in the closing of tourism infrastructure and limited mobility in both land and coastal areas. We used this “natural experiment” as an opportunity to study the impact of tour-boat activities on dolphin communication by using passive acoustic monitoring data collected before and during the lockdown at Dolphin Bay, Bocas del Toro, Panama. During the lockdown, tour-boat activity was absent, but boats transporting people and supplies were allowed to circulate. The shift in type of boat activity within the lockdown resulted in lower ambient noise levels and more frequent detections of dolphin sounds. We also detected a more diverse whistle repertoire during the lockdown than in the pre-lockdown period, even when accounting for variation in sample coverage. A Random Forest Analysis classified whistles between the two periods with high accuracy (92.4% accuracy, κ = 0.85) based primarily on whistle modulation and duration. During the lockdown, whistles were longer in duration and less modulated than pre-lockdown. Our study shows that a shift in boat traffic activity can generate significant changes in dolphin habitat, and in their communicative signals, an important consideration given ongoing unregulated ecotourism in the region.