As the third soybean-producer state in Brazil, Rio Grande do Sul (RS) presents a known year-on-year unevenness for soybean production, mainly due to water availability. This study aimed to assess the weather effects, with special focus on rainfall during 25 soybean growing seasons and 11 producing regions around the State. Sites were divided into three Clusters according to soybean yield and the effect of El Niño Southern Oscillation (ENSO) was considered in association with soil water balance. Neutral ENSO phases occurred in 32% of the years, while El Niño and La Ninã occurring in 36% and 32% of the years, respectively. Seasons under El Niño normally present higher accumulated rainfall, whereas those under La Niña present a reduction. Data from neutral-year sites of Clusters B and C seems to be more disturbed. No season had statistical difference of rainfall among Clusters under Neutral conditions. In addition, thermal gradient in RS from October to January benefited sites of Cluster A. Interaction of soils with higher water-storage capacity and cooler temperature reduces the water consumption by soybeans, causing lower values of water deficiency. A boundary function relating soybean yield and rainfall displays the limit of 800 mm for significant yield increments, and such amounts of rainfall were only achieved in El Niño seasons. The combined effect of rainfall and soil type on soybean yield, represented by the actual soybean yields-water deficit relationship, led to water propitiate from -3.7 to -15.2 kg mm-1 ha-1. Decision-making on public policies and investments on the soybean industry can be supported from our results, either to better planning the investments on the soybean farming systems depending on the ENSO phase predictions, either to reduce the production risks in the region inherent to local weather.