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The nature of the nutrient budget for temporary rivers differs from that for permanent rivers because of the restricted nature of flow, the lack of adequate dilution, and weather conditions which are conducive to the development of algal blooms. We analyse the nutrient budget of three tributaries of a temporary river in Cyprus, the Kouris, with the aid of the MONERIS model. MONERIS in-stream retention module was modified to account for a 1-dimensional advection - dispersion pollutants transport rather than the general mass balance equation for mixed reactors. TRS plot classified Kryos stream as an Intermittent flow - Dry (I-D) stream (hydrologically altered) and Kouris and Limnatis as Intermittent - Pool (I-P) streams that need different lumped parameterization in MONERIS simulation. Point sources are important for nitrogen (64 %) and phosphorous emissions (22 %), and diffuse sources for nitrogen via erosion (15 %) and free grazing (12 %) and for phosphorous via free grazing (8 %). We estimate that around 40 % of N and 88 % of P entering streams is retained in the stream. An analysis of the model uncertainty and sensitivity to input data indicates that MONERIS model, even in semi-arid areas, may be used for the purpose of managing river basins.