The biotic ligand model (BLM) was used to assess copper (Cu) bioavailability, toxicity, water-effect ratios (WER), and Cu site-specific water-quality criteria (SSWQC) in the Matanza River and Pilcomayo River, Argentina, where anthropogenic inputs and natural phenomena have led to high concentrations of chemical species capable of reducing metal toxicity: Sodium, total hardness, alkalinity, dissolved organic carbon, and suspended particulate matter (SPM), as well as other metals. The purpose of this study was to evaluate the feasibility of developing Cu-SSWQC from a modified scenario of the BLM–Monte-Carlo method model. The response of the BLM model in these rivers, with water quality near its application boundary conditions, was evaluated during the 2003 to 2004 hydrological cycle. Cu toxicity tests were conducted with Daphnia magna as the test organism. The BLM (Version ap08) toxicity estimates for D. magna were within a factor of 2 of the line of perfect agreement with toxicity test results, although highly variable relevant water-quality parameters showed that mean estimates were more than 2 times the mean 50% effective concentration (EC50) derived from the corresponding toxicity tests. Suspended particulate matter was an important sink for Cu added to unfiltered water of the Pilcomayo River, but it also exerted some toxic effect. Minimums WER, estimated with a modified scenario of the BLM-MONTE, ranged from 1.5 (Pilcomayo River, at Misión La Paz) up to 11 (Matanza River, at Route 3). The corresponding Cu-SSWQC values were 30 and 105 μg/L, respectively.