In this study, the impacts of irrigation water quality and soil characteristics on paddy rice yields were investigated. Standard spectroscopy and spectrometry methods were used to analyze irrigation water and irrigated soil samples. The irrigation water had sodium adsorption ratio (SAR) values ranging from 0 to 3. The corresponding electrical conductivity (EC) values were between 0.2 and 0.7 dS/m and accounted for 14% of all samples—posing slight to moderate infiltration problem. Neither Na+ nor Cl− levels were high enough to cause toxicity problems in the irrigation water. For B, 54% of the samples were found to have moderate toxicity whereas ~ 14% of the samples indicated severe B toxicity in the irrigation water. For bicarbonate, about 86 and 14% of the irrigation water indicated slight-to-moderate and severe potential detrimental effect to plant growth, respectively. All trace elements in the irrigation water were too low to cause any harmful effect. Although soil EC, organic carbon (OC), and pH indicated favorable level, there were high standard deviation (SD) values in soil Fe and Zn. The mean value of Fe in soils was 19.8 mg/kg, indicating signs of Fe-deficiency. High SD values were also found in the total N (TN) content of the studied soils. Furthermore, a low soil K content was observed in the analyzed soil samples. Appropriate fertilizer application for improving nutrient deficiencies in the study area is highly recommended. Furthermore, on-farm management practices need to be guided by scientific findings from the present as well as other studies.