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Monthly water balance accounts (1990-2006) were developed for 145 river reaches within the Murray-Darling Basin (MDB) as part of the Murray-Darling Basin Sustainable Yields project. They were used to assess how well river hydrology is measured and understood, and to identify the main uncertainties in river modelling. The purpose of accounting was different compared to water accounting systems set up for natural resources management, such as those that will be produced by the Bureau of Meteorology. Many aspects are still relevant however. A brief overview of the methods and data sources is provided, with emphasis on the methods used to combine different data sources in water balance accounts. Some benefits of the approach taken were identified as well as deficiencies requiring improvement. The aggregate water balance accounts are presented for all reaches that could be assessed, which covered most but not all of the MDB's river sections. The components of the water balance for which on-ground hydrometric data are available were compared to those which could be attributed with less direct observations, and apparent gains and losses that could not be attributed, respectively (noting that these will have included both real water and estimation errors in all terms). Approximately 48% of the overall water balance appeared to be gauged. Another 21% could be attributed, whilst the remaining 31% was unattributed. Comparison of the accounted and simulated water balance was not straightforward but provided useful insights into the assumptions made in modelling, and the uncertainty in these assumptions. Some implications for 'formal' water accounting are discussed. Unlike perhaps financial accounting, all numbers in a water account will be indirectly derived using estimation methods, because (1) every hydrological observation is indirect and involves a varying degree of estimation; and (2) not including even more indirect estimation methods (e.g. hydrological models) will produ