Embodied water in a socio-economic system refers to the hidden water contained in products traded from one region or one sector to another and has been the center of concern for water management in recent years. However, most models developed for water system analysis ignore cycling and indirect flows, making it difficult to explain the effects of structure on these factors among sectors. Therefore, those models fail to examine the water utilization efficiency from an integral view. In this study, we investigate an embodied socio-economic water system using network analysis developed originally for ecological systems. In this manner, we identify structural and throughflow indicators, such as Finn Cycling Index, Indirect effects ratio, and aggradation, to show the efficiency of water utilization. The three indicators show different perspectives of the system's efficiency change over time, indicating that only the combination of these three indicators can provide a holistic portray about efficiency. Results showed that the structure influenced the cycling and indirect flows, and from a throughflow perspective, the system depends on large boundary inputs of fresh water. Furthermore, the values of Cycling Index and Indirect effect ratio are much lower than for natural food webs, implying that the policies that led to the structural change and reduction of boundary fresh water inputs do not lead to positive water utilization seen in natural systems. This study provides a novel perspective and methodology for assessing the structure and efficiency of water utilization system with a whole perspective.