The study of the environmental quality of the largest rivers such as the Paraná, is a challenge for the different disciplines of environmental sciences. Considering that the water quality of the largest rivers is mainly affected by the contributions of pollutants through the tributaries, we evaluate, using a multidisciplinary approach, the environmental quality of the tributaries of the Paraná River in Argentina, whose subbasins are associated with different levels and types of anthropization. We also discussed the aptitude of different diagnostic tools used to study the quality of water courses associated with rural landscapes and proposed a new indicator of easy measurement to quantify the level of anthropization in these environments. We selected 6 sampling sites (SM) related with different level of anthropization, considering agricultural and/or livestock (A/G) and urban or industrial (U/I) activities. The general parameters of water quality were measured in situ, and water and sediment samples were taken for physical, chemical, microbiological and ecotoxicological evaluation. The toxicity was evaluated by a battery of bioassays (Daphnia magna, Hyalella curvispina and Lactuca sativa). The frequency of bioassays that show significant effects correlated positively with anthropization. Lactuca sativa was particularly sensitive to pollutants of A/G origin, while crustaceans, to those from U/I. The combination of U/I and A/G activities increased the toxicological complexity of the watercourses, producing greater adverse effects. Although, in the rural areas the U/I activities represented a scale notably small in relation to A/G, their contribution to the deterioration of the toxicological quality of watercourses appeared significant.