Quantification of water losses (WL) in water distribution networks (WDNs) is a crucial task towards the development of proper strategies to reduce them. Currently, WL estimation methods rely on semi-empirical assumptions and different implementation strategies that increase the uncertainty of the obtained estimates. In this work, we compare the effectiveness and robustness of two widely applied WL estimation approaches found in the international literature: (a) the water balance, or top-down, approach introduced by the International Water Association (IWA), and (b) the bottom-up or minimum night flow (MNF) approach, based on a recently proposed probabilistic MNF estimation method. In doing so, we use users’ consumption and flow-pressure data from the 4 largest pressure management areas (PMAs) of the WDN of the city of Patras (the third largest city in Greece), which consist of more than 200 km of pipeline, cover the entire city center of Patras, and serve approximately 58,000 consumers. The obtained results show that: (a) when MNF estimation is done in a rigorous statistical setting from high resolution flow-pressure timeseries, and (b) there is sufficient understanding of the consumption types and patterns during day and night hours, the two approaches effectively converge, allowing for more reliable estimation of the individual WL components. In addition, when high resolution flow-pressure timeseries are available at the inlets of PMAs, the suggested version of the bottom-up approach with probabilistic estimation of MNF should be preferred as less sensitive, while allowing for confidence interval estimation of the individual components of water losses and development of proper strategies to reduce them.