The currently available methods for the assessment of the eutrophication degree are expensive, time-consuming and require advanced laboratory equipment and knowledge. The aim of this work was to determine a simple and economically justified method of monitoring the effects of eutrophication of water in the agricultural area and linking the results of monitoring physicochemical parameters of water with chlorophyll fluorescence as a potential health risk on the basis of established alarm levels. The research was conducted in water reservoirs located in the rural area, differing in the intensity of exploitation of adjacent areas: located in the vicinity of intensively cultivated areas and in the protected area of ​​the nature reserve. The work determined the efficiency of the photosynthetic apparatus of algae and physicochemical properties of water. The studies have shown that the increase in the chlorophyll fluorescence intensity is associated with an raised biogenic load and an increased occurrence of chlorophyll-containing micro-fractions. The results indicate the possibility of using chlorophyll fluorescence measurements to assess the degree of water eutrophication. The presented method can be used for a non-invasive, quick and precise assessment of the physiological status of water ecosystems in rural areas, particularly vulnerable to the eutrophication processes.