Collaborative projects under the Horizon Europe Framework Program of the European Union typically involve a large number of partners from multiple countries. Data-centric projects, among them, often require integration of disparate data source formats and collection methods, leading to complex data management architectures and policies. This article is an extended version of an article presented at the 1st International Conference on Big Data Analytics and Applications (BDAA’2025). It explores design decisions, organisational principles, and technological solutions to address these challenges by focusing on data integration of data sources and the hybridisation of data services. This experience was gathered while working on DiverSea, a project dedicated to the analysis of biodiversity dynamics along European coastlines—ranging from the Black Sea to the Mediterranean and the North Sea. While grounded in established technologies, the project’s takeaways offer valuable insights for environmental data projects across aquatic, terrestrial, and atmospheric domains.