Chlorophyll-a concentration and physico-chemical water quality of water bodies surrounding Santa Fe City (Argentina) were analyzed at 20 sampling sites during different hydroclimatic periods (August-September 2005, March-April 2006). Areas with different water quality were separated by Euclidean cluster analysis, and correlation among both environmental and chlorophyll distance 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 was registered in comparison with previous studies, and chlorophyll-a concentrations are similar to those encountered in other eutrophicated rivers of the world. The oligo-mesotrophic level found at the Setúbal shallow lake was lower than expected due to the nutrient contents and human activities of its basin. However, the incoming of pristine waters from the Paraná System produces a sweeping effect and a semi-lotic lake behavior that impedes eutrophication enhancement. During high-waters this river also improved water quality of Santa Fe and Coronda Rivers. The chlorophyll-a diminution at Setúbal Lake and Santa Fe River in comparison to earlier studies, may be also explained by the introduction in the last decade of the bivalve Limnoperna fortunei that could be responsible of important losses of algal cells. Although trophic state according to chlorophyll-a concentration was improved with discharge increments, nitrate and total phosphorus concentration augmented in most sites as a result of the input from polluted flooded areas. The higher ranges encountered in the present study either of chlorophyll-a or nutrient content, indicate changes in water quality and a resultant eutrophication process over a period of decades. The health of water bodies is not yet in danger, but it is declining due to induced man-changes.