In Indonesia, tourism has become a promising major economic sector, particularly because of its contributions toward developing the economy and creating employment opportunities for local communities with rich coastal ecosystems. However, the balance between the environmental, social, and economic realms has come into question, as unsustainable tourism practices continue to be promoted in Indonesia. To address such challenges, it is important to identify tourism impacts and provide sustainable policies and plans. Communities often record tourism impacts through their perceptions and act as important stakeholders in the process of sustainable tourism development. We examined tourism impacts on coastal ecosystems in Karimunjawa from the perspective of local communities. More comprehensively, we investigated their perceptions from three perspectives: socio-cultural, economic, and environmental. The study results revealed that the respondents held positive perceptions about tourism’s impact on socio-cultural and economic sectors and negative perceptions about its impact in the environmental domain. A chi-square test and Spearman’s correlation analysis indicated that the respondents’ educational attainment and tourism involvement influenced their perceptions on these issues. The current study results could be used as a baseline reference for contextualizing sustainable tourism plans regarding small island ecosystems in Indonesia.