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Discharges from wastewater treatment plants have been cited as one of the point sources contributing to surface water quality deterioration. However, does high-quality effluent affect water quality, and contribute significantly to nutrient enrichment or the eutrophication of receiving waters? The Vltava River and a wastewater treatment plant in the Czech Republic were used in a case study, to try to answer these questions through water quality indices and source identification. Samples were collected upstream and downstream of the effluent discharge point, and analyzed for temperature, pH, dissolved oxygen, chemical oxygen demand, nitrate, nitrite, ammonium, phosphate and sulfate. No statistically significant difference (P > 0.05) was observed between most of the upstream and downstream samples’ physicochemical characteristics. The water quality, organic pollution, and eutrophication indices of the river, upstream of the effluent discharge point were 83.48, 2.05 and 2.67, respectively, but increased to 99.06, 2.87 and 3.74 downstream. Nutrient source identification using principal component analysis suggests that the increase might be due to the effluent discharge. However, the river's comprehensive ecological (quality classification) status was the same upstream as downstream, indicating that the discharged effluent did not cause nutrient enrichment of the river.