Touristic whale watching (WW) is an important socioeconomic activity worldwide. Recently, short and long-term impacts caused by WW have been reported for several cetacean species, including Delphinus delphis and Tursiops truncatus, the two most observed species in Portugal. Most of the operations in mainland Portugal are concentrated on the South Coast (Algarve). However, despite their importance for the region, studies focused on the impact of this activity on the animals are still scarce. We used acoustic behaviour analysis and land-based observations to determine the alterations in the vocalization patterns of these animals caused by WW vessels and the length of exposure to this stressor. We found WW presence significantly altered five out of six acoustic parameters of whistles, whistle rate, and whistle type distribution for D. delphis, whereas T. truncatus exhibited significant changes in three acoustic parameters. Conversely, T. truncatus significantly reduced echolocation click rates, while D. delphis did not show significant changes. We also found that the Central region of this coast is the most affected, with animals exposed to WW vessels for up to 38.9% of daylight hours. Furthermore, 66.7% of the observation time in this area had several vessels that exceeded the limit established by law. These results suggest that our study species are impacted by WW, while D. delphis is more affected during social behaviours, and T. truncatus is more affected during foraging activities. Both behaviours are biologically significant, and their disturbance might, in the long term, lead to adverse effects at the population level by decreasing reproductive success and fitness. A gap in knowledge, inadequate legislation and compliance issues threaten the development of a sustainable WW industry in the Algarve and might endanger local populations, therefore immediate attention is needed.