Chlorophyll-a concentration and physico-chemical water quality of water bodies surrounding Santa Fe City (Argentina) wereanalyzed at 20 sampling sites during different hydroclimatic periods (August-September 2005, March-April 2006). Areas withdifferent water quality were separated by Euclidean cluster analysis, and correlation among both environmental and chlorophylldistance matrices were found (p<0.01). The areas more affected by anthropogenic influence, Los Saladillos and Salado Rivers,reached the highest trophic level as regards to chlorophyll concentration. Acceleration in the eutrophication process wasregistered in comparison with previous studies, and chlorophyll-a concentrations are similar to those encountered in othereutrophicated rivers of the world. The oligo-mesotrophic level found at the Setúbal shallow lake was lower than expected due tothe nutrient contents and human activities of its basin. However, the incoming of pristine waters from the Paraná Systemproduces a sweeping effect and a semi-lotic lake behavior that impedes eutrophication enhancement. During high-waters thisriver also improved water quality of Santa Fe and Coronda Rivers. The chlorophyll-a diminution at Setúbal Lake and Santa FeRiver in comparison to earlier studies, may be also explained by the introduction in the last decade of the bivalve Limnopernafortunei that could be responsible of important losses of algal cells. Although trophic state according to chlorophyll-aconcentration was improved with discharge increments, nitrate and total phosphorus concentration augmented in most sites as aresult of the input from polluted flooded areas. The higher ranges encountered in the present study either of chlorophyll-a ornutrient content, indicate changes in water quality and a resultant eutrophication process over a period of decades. The health ofwater bodies is not yet in danger, but it is declining due to induced man-changes.