With increasing water scarcity and the need for sustainable agricultural practices, the reuse of treated wastewater for irrigation has gained attention. Although there are studies on the short-term effects of wastewater irrigation, limited research focuses on the long-term implications across various crop seasons in drainage basin regions. Hence, this study examines how the crop season has influenced changes in soil characteristics and plant nutrient levels of sorghum and soybean crops after 40 years of continuous sewage water application. The research employs a longitudinal field study where soil samples are collected regularly from plots irrigated with sewer water. Plant samples were also analyzed for nutrient concentrations to evaluate the impact on crop growth. Various analytical techniques, such as soil testing, plant tissue analysis, and statistical methods, are utilized to interpret the data. The study showed that 40 years of continuous application of sewage water significantly impacted the crops’ different soil qualities and plant nutrients, specifically soybeans and sorghum. Similarly, the other soil characteristics and nutrient levels of both crops were equally impacted by the agricultural season (rabi and kharif ). While the values of bulk density, exchangeable K, and sulfur were greater in the kharif season, higher levels of pH, EC, organic carbon, calcium carbonate, CEC, N, and P were discovered in the rabi season. The grains of sorghum and soybean crops included higher levels of N, P, and S, but the straws of the same crops contained higher levels of K. The study emphasizes the importance of monitoring soil health and plant nutrition when using sewer water for irrigation in drainage basin areas. Long-term wastewater application can positively and negatively impact soil fertility and crop productivity, emphasizing the need for sustainable management practices. Future research could explore the mechanisms underlying these changes and investigate potential remediation strategies to mitigate adverse effects.