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Lakes and reservoirs (impoundments) are often viewed as a sink for nutrients within the river continuum. To date, most studies on nutrient retention within impoundments are derived from the temperate climate zones of Europe and North America, only consider one nutrient, and are often short-term (1-2 years). Here, we present a long-term (17 year) data set and nutrient (nitrogen, phosphorus and silica) budget for two connected semi-arid lakes (the Lower Lakes) at the terminus of the River Murray, Australia. Most of the filterable reactive phosphorus and nitrate entering the lakes were retained (77 and 92%, respectively). Total phosphorus (TP) was also strongly retained (55% of the annual TP load on average) and the annual TP retention rates could be predicted as a function of the areal hydraulic loading rate (annual lake outflow/lake surface area). On average, there was a slight net retention (7%) of the annual total nitrogen (TN) load but a slight net export (6% of the load) of organic N. TN retention as function of the areal hydraulic loading rate was lower than expected from existing models, possibly because of high nitrogen fixation rates in the Lower Lakes. Silica was retained (39%) at similar rates to those observed in previous studies. There was also a marked increase in the TN:TP and TN:Si ratios within the lake (TN:TP similar to 30 and TN:Si similar to 0.67) compared to those entering (TN:TP similar to 15, TN:Si similar to 0.45), as a consequence of the relatively low net retention of nitrogen.