Since coastal zone is the transitional ecotone between land and sea, where the contradiction between ecological protection economic development and resource utility is sharp, an ecological and environmental monitoring network is extremely important for local environmental pollution control and ecological protection, and it is also fundamental to sustainable development in coastal zones. Taking the Jiulong River and adjacent Xiamen Bay in southeast China as a demonstrative area for land and sea coordination and to overcome the inadequacy of the current conventional monitoring systems, this study established an integrated ecological monitoring network in the Jiulong River-Estuary continuum and nearshore areas for comprehensively monitoring both local environmental factors and ecological ecosystems based on the current conventional monitoring systems. This network was performed through combination of monitoring using remote sensing and biological techniques, bridging gaps of water quality standards between territorial and adjacent sea, comprehensive field samplings and invents of innovative measuring equipment, and setup of online observation system. The integrated monitoring network was capable of management and measurement from pollutant sources, environmental quality, crucial ecosystems, and landscape levels. This firstly constructed integrated-monitoring system component is ecosystem-based and incorporated organism, water, and sediments monitoring for this river-estuary-bay continuum. Secondly, a series of nutrient criteria/standard including dissolved inorganic nitrogen and soluble reactive phosphorus for the different estuarine salinity segments in the estuary were proposed. Thirdly, targeting at the objective of total pollutant discharge controlling between land and sea, an online pollutant fluxes monitoring system between the interfaces of the Jiulong River and its estuary were constructed. On the basis of combination of dynamic monitoring using remote sensing observations and field investigations, as the fourth step, an ecological monitoring system was also established. Then based on the above four monitoring systems and observed results, an ecological indicator system including parameters from coastal lands, estuarine and nearshore areas for rapid evaluating regionally ecological security was proposed. This indicator system was then applied to dynamically evaluate regionally ecological security and sustainable development for the Jiulong River and Xiamen Bay. Finally, the above several monitoring systems have been integrated and successfully applied in the areas across from territorial (watershed) to estuarine (nearshore) areas, and from management and measurement of pollutant sources, environmental quality, crucial ecosystems, and to landscape levels. Therefore, this integrated monitoring network would significantly facilitate environmental quality improvement, pollution control, total pollutant discharge control, ecological protection, ecological security evaluation, and restoration in coastal areas from the perspective of scientific support.