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Individuals from cetacean populations regularly using inshore waters can be more vulnerable to anthropogenic pressures than those living in offshore areas. The monitoring of Good Environmental Status within the European Marine Strategy Framework Directive (MSFD) requires assessing demographic parameters of these local populations. Therefore, a two-step framework was developed for this monitoring and applied to a long-term photo-identification database of short-finned pilot whales in the inshore waters of Madeira. First, a standardized method to identify site fidelity structures based on K-means analysis was used to determine the local population, i.e., individuals with higher site fidelity. Then, demographic parameters were estimated over 15 years using a robust design model. Finally, the effect of increasing whale watching boats as a potential threat was tested. The results revealed no temporary emigration, showing that the site fidelity methodology could accurately identify the local population. Adult survival rates were high and abundance estimates were stable. Therefore, these results should be used as a baseline for future MSFD cycles. No negative effect of whale watching was found on demographic parameters for adult individuals. However, young animals, which could be more vulnerable to local pressures, were not fully included in the analysis, and potential effects on reproduction output were not studied. Therefore, an adverse effect of whale watching on the local population cannot be ruled out. This monitoring framework should be applied to other species and study areas to confirm its wide application to help management decisions reaching better conservation status for cetacean species. [ABSTRACT FROM AUTHOR]