In the light of climate changes and in order to achieve stable crop production, irrigation represents an inevitable measure. Apart from water quantity, water quality represents a matter of concern. The paper elaborates on the presence of iron and manganese, as the main factors of causing the clogging of irrigation systems. The examined well water samples were taken mainly from Serbia. Photometric methods were applied for determining iron and manganese, and sensors for pH and conductivity. The obtained values were later subjected to a classification for irrigation water and the well water samples were classified according to the given thresholds. Precise location and presentation of the obtained results were done using the Geographic information system. The research has shown that from the analysed well water, only in 6 samples iron concentrations were increased up to a level classified as “extreme restrictions,” 4 samples as “warning,” while 31 samples of water were “adequate for irrigation.” Concerning manganese, in only one sample water was classified as “extreme restrictions,” in 14 as “warning” and in 26 as “adequate for irrigation.” pH and conductivity did not coincide with elevated concentrations of iron and manganese, but in the cases of exceeding thresholds, special attention should also be paid to these parameters.