Evaluation of site specific drip fertigation system based on GIS integrated nutrient status maps was conducted at Instructional Farm, KCAET, Tavanur, Malappuram, Kerala. Using the spatial variability maps of the soil nutrients, two test plots, one from high fertility zone and one from low fertility zone were identified with the help of GPS for raising the tomato crop. The experimental plot was laid out in a Completely Randomized Design (CRD) with four treatments and four replications. The results showed an increase in yield and growth parameters under site specific drip fertigation treatment in low fertility area due to the adequate fertiliser application than general recommendation. In high fertility area, reduction of fertilizer to site specific requirements has produced almost similar result of general recommendation which indicates that site specific dose was sufficient to produce optimum yield from the crop. Site specific drip fertigation helped to achieve a higher water and nutrient use efficiency with a high economic return of agricultural produce. From this study, it could be concluded that, instead of going with blanket nutrient recommendation, a site specific nutrient recommendation may help the farmers who want to achieve higher profit from unit land area by using optimum inputs, thereby reducing environmental stress due to over fertilizer application.