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• Half of Latin American scientists are not addressing the land-sea systems as a whole. • Communication of scientists with stakeholders across environments is deficient. • Governance schemes are compartmentalized and do not align with ecological linkages. • Institutional instruments and intermediaries' involvement foster holistic governance. • Boundary work and trade-offs modeling may mainstream ES concept to policy. The concept of Ecosystem Services (ES) highlights that human wellbeing depends on nature and is a 'whole system aware' view. Land-sea systems are examples of complex systems including interfaces that can be perceived as boundaries, overlooking connections of the whole system. We explored the occurrence of several features of scientific knowledge building and governance of these systems that can hinder the recognition of connectivity, challenging an ES approach. We analyzed online survey responses from academics representing 22 research institutions and 13 case studies, all from Latin America. Results showed that the generation of scientific knowledge is not integrally approached and there are deficiencies in researchers' communication with stakeholders across the land-sea interface. These drawbacks in scientific knowledge building could be one of the reasons why an ES approach is rarely applied on governance of land-sea systems. The cases showed segmented governance schemes and that conflict situations enhance the visibility of ecosystem relations. The establishment of long-lasting institutional instruments and the involvement of intermediaries connecting sectors are complementary paths to improve integrated governance. Using ES as a boundary concept could improve integration between sectors and ES trade-off analysis can help to introduce ecosystem relations to stakeholders related to their own interests. [ABSTRACT FROM AUTHOR]