In terms of farm fertilizer Consumption, India is the world’s second largest country after China. Reducing fertilizer use cannot be considered a viable option, since optimizing food output was the highest priority for the population’s food and nutritional protection. Nitrogen, Phosphorous and Potassium fertilizers are farm fertilizers and are in great demand in Indian agriculture. This study investigated the effect of rainfall dynamics on farm fertilizer transport for rainfed Cotton Crop in Semi-arid Region in the Raichur district of South India. The solute transport and reaction parameters were assessed at the depths of 50, 100 and 150 cm of soil column. Hydrus-1D and Hydrus-2D software has been used for modelling transport of fertilizer in vadose zone. Rainfall data from 2015 to 2020, Soil data, Crop data, Soil hydraulic parameters, and Solute data has been used for this study. Results suggested that solute transport for average actual precipitation, 20% decreased precipitation and 20% increased precipitation at 150 cm depth of soil column was 0.000109, 0.00000000424, 0.000371 mmol cm−3 for nitrogen fertilizer, 0, 0, 0.00000014 mmol−3 for phosphorous fertilizer and 0, 0, 0.0000000329 mmol−3 respectively for potassium fertilizer. From this, it can be inferred that increased precipitation caused solutes to move more quickly than usual. Therefore, it can be concluded that due to climate change, changes in rainfall patterns and increased rainfall intensity might lead to excessive leaching of agricultural fertilizers into the vadoze zone and groundwater.