Our research is devoted to development of information infrastructure for e-service semi-automatic provision by using distributed data warehouses (DWs) of water protection domain. Development of software for semi-automatic service provision is based on artificial planner and structure of goals adapted for specialized needs of end users. Such e-service preparation mechanism can work under the unified coherent framework for solving the environment protection problems by evaluation of the processes of water consumption and contamination. The possibilities of integration of distributed DWs of water management sector into web portal meeting the requirements of conceptual interoperability are presented. Design approach is based on development of decision support system (DSS) that is designed as multilayered system with multi–componential, interoperable structure of databases (DBs), which are under responsibility of different public administration institutions such as European Environment Information and Observation Network (EIONET) and national environment protection agencies. The infrastructure of EIONET is used for supporting and improving data and information flows. The Water resource management information system (WRMIS) became the kernel component of DSS. WRMIS prototype facilitates data flows between the institutions and gives access to data for relevant institutions and the public providing e-services using proposed DSS. The research investigations are made according to the requirements of European Union Water Framework Directive, Sustainable Development Strategy and ReportNet as the EIONET infrastructure for supporting and improving data and information flows. Additional means are integrated in the structures of DSS as knowledge representation techniques based on conceptual schemas, data flow diagrams, and decision-making rules. The on-line management techniques are based on assurance of interoperability by using Open Web Platform W3C standards for web service development, such as XML, SOAP, HTTP, etc.