The U.S. Integrated Ocean Observing System is being designed to be an end-to Dend, integrated, sustained, operational System of Systems that provides data, information and products to benefit a broad range of stakeholders in their decision-making. These design concepts form the basis of pilot projects being undertaken by the Gulf of Mexico Coastal Ocean Observing System Regional Association (GCOOS-RA). This paper presents a case study of the GCOOS-RA Harmful Algal Bloom Integrated Observing System (HABIOS) Project. A set of research activities related to harmful algal blooms is examined for eventual transition from pilot project to an integrated operational system. The end-to-end nature of the system is explored from the perspectives of design and operation, data management and communication, modeling and analysis, decision-support tools and outreach, and benefits to stakeholders at national, regional, state, and local levels. The case study of the HABs pilot projects will demonstrate that HAB-related observations need to be both sustained and operational, and that progress is being may through the integration of the efforts of many entities concerned with detecting and monitoring HAB events and mitigating HAB impacts.