The growing scarcity of freshwater represents an increasing risk to human society. Water scarcity is often presented as a systematic water scarcity, which is often caused by complex factors. Most previous researchers have focused on either available or virtual water in order to design strategies for mitigating water scarcity; however, herein, we argue that systematic water scarcity due to urbanization requires an assessment of the integrated metabolic efficiency of available and virtual water. In the case of Xiamen City, which is located in the shadow area of the rain belt in the subtropical monsoon climate, the dry years of 2003, 2009, and 2011 were selected for the assessment in order to implement the results in water management policies and mitigation measures for systematic water shortages. Material flow analysis (MFA) was employed to analyze integrated flows of urban available and virtual water in the dry years from the perspective of water metabolic processes or patterns. It was found that MFA could derive effective indicators for the integrated assessment, based on the comparable, comprehensive, and verifiable MFA charts, according to the effects of indicators in identifying critical pathways and links of the integrated flows. Using these MFA indicators, an indicator system could be formulated following the trade-off between socio-economic and environmental benefits. Finally, the indicator system was empowered by the analytic hierarchy process and was used in the integrated assessment. The results showed that improvement in efficiency of the integrated metabolism was accelerated in the past 10 years, and this was dominantly driven by key indicators that evaluated the socio-economic benefits of water use (irrigated area per cubic meter of water, industrial output per cubic meter of water, retail sales of consumer goods per cubic meter of water) and assessed the function of water metabolic processes or patterns (freshwater reuse rate, the proportion of water used in the ecosystem to that used in socio-economic system). These indicators show that the improvement in water metabolic efficiency was dependent on the positive adjustment of water use mode, structure, and process. Scenario Analysis was applied in the design of a better urban water metabolic management system, based on the key driving indicators derived from the integrated assessment results. The indicator system proved robust and operational, and reflects the interaction between natural and social water cycle. In addition, it allows dynamic interaction between water flow and the related socioeconomic or environmental processes to be analyzed, and therefore, could be used to formulate water management policies or developing urban water metabolic models with high efficiency. Establishment of indicator systems based on MFA results in this case study would open a new window for the development of operational efficient indicator systems.