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These days with population growth and consequence of water shortage, treated wastewater is used as an alternative source in agricultural and industrial purposes. Moreover, emerging and growing impacts of climate change, which have exacerbated the climate hazards, have placed a challenge to the management of hydrosystems including waste water treatment plants which provide treated wastewater Therefore, ensuring the proper performance of these facilities, in terms of acceptable effluent concentration, is imperative. This objective could be achieved by assessing the systems reliability, from standpoint quality of effluent, namely successful performance of facility within acceptable quality standards. This study presents a quantitative and qualitative framework for obtaining the reliability of three different waste water treatment plants at the times of coastal flooding. Coastal flooding can cause a failure in WWTP in two different ways; first by large inflow discharge resulting in solids washout and consequence performance reduction called quality failure and second, the destruction of unit operations imposed by large storm surges which inundates plants' structural components. For quantitative method, load resistance approach is used which incorporates the probability nature of both exerted load on the system and the resistance of the infrastructure. While in previous studies these two terms are considered independent, in this study, some dependencies are considered between load and resistance. The dependencies can be modeled by utilizing copula theory. The effect of each unit operation in plants performance is investigated by estimating the level of units' performance during time of storms. Regarding qualitative approach, a fault tree analysis is utilized. This approach uses a backward analysis beginning with a system failure as a top event and traces backward, searching for possible causes of the failure which gives a good insight into design and operation of any infrastructure in a way that suitable measures could be implemented. This could decrease the effect of important factors in the system's failure. The case study is three waste water treatment plants in Brooklyn borough in New York City. Results showed significant value of using reliability methods in assessing infrastructure performance at the time of floods.