In this paper, there was determined the impact of agriculture-derived biogenic components on the quality of raw water abstracted by the Water Treatment Plant, a facility of the Municipal Waterworks and Wastewater Systems in Kraków (referred to as MPWiK) during a period from 2007 to 2011. The following water parameters were determined in water samples from the Rudawa river, the artificial Lake of Dobczyce, and the Dłubia and Sanka rivers: turbidity, ammonium nitrogen, nitrites, nitrates, Kjeldahl nitrogen, total nitrogen, phosphates (V), total phosphorus, and chlorophyll a. Based on the results of the analyses performed during those 5 years, statistically significant differences (p < 0.05) were found among the mean values of all the raw water quality indicators. The contents of nitrates and phosphates(V), analyzed at one month intervals for the duration of 60 months, made it possible to draw trends. A slightly descending trend of low values occurred in the case of nitrates contained in the Lake of Dobczyce water, whereas the waters in the Rudawa and Dłubia rivers were characterized by a trend showing steady, but higher values. The highest fluctuations in the content of nitrates were determined in the water of the Sanka river; the maximum value of this indicator (34.91 mg·dm^-3) was reported in the 28^th week of performing the analyses. Then again, the mean-monthly content level of phosphates (V) in the waters from the sources analyzed during a 26 week period hardly ever exceeded 0.29 mg·dm^-3. Beginning in the 27th week, a disruption occurred in this trend causing high coefficients of variation to appear regardless of where the water samples were taken from. The variations in the content of phosphates in the Lake of Dobczyce water, C_v = 532 %, were the highest, although the maximum content of this component in the Lake water, expressed as an absolute value, was two or three times lower than the maximum content thereof in all other waters analyzed. The eutrophication degree was assessed according to the legal standards and based on the annual biogenic indicators. The highest mean annual content of total nitrogen (1.72 mg·dm^-3) was reported in the Rudawa river waters in 2009. Moreover, the highest mean annual content of total phosphorus was also reported in the Rudawa river water in 2007 (0.19 mg·dm^-3). The highest amounts of chlorophyll a (3.26 µm·dm^-3) were determined in the Sanka river waters in 2010. Of all the indicators analysed, no indicator exceeded the normative standard level above which the eutrophication would take place. But the eutrophication process was found in the waters of the Rudawa, Dłubnia, and Sanka rivers; the mean annual contents of nitrates were higher than the limit value of 10 mg·dm^-3. Despite the eutrophication in those three rivers, their raw waters were not classified as waters in danger of being polluted by agriculture-derived nitrogen since the content of nitrates in any of the samples studied did not exceed the limit values of 40 to 50 mg of NO₃·dm^-3 as determined in the regulation issued by the Minister of the Environment.