Abstract Transverse mixing coefficient (TMC) is known as one of the most effective parameters in the two-dimensional simulation of water pollution, and increasing the accuracy of estimating this coefficient will improve the modeling process. In the present study, genetic algorithm (GA)-based support vector machine (SVM) was used to estimate TMC in streams. There are three principal parameters in SVM which need to be adjusted during the estimating procedure. GA helps SVM and optimizes these three parameters automatically in the best way. The accuracy of the SVM and GA-SVM algorithms along with previous models were discussed in TMC estimation by using a wide range of hydraulic and geometrical data from field and laboratory experiments. According to statistical analysis, the performance of the mentioned models in both straight and meandering streams was more accurate than the regression-based models. Sensitivity analysis showed that the accuracy of the GA-SVM algorithm in TMC estimation significantly correlated with the number of input parameters. Eliminating the uncorrelated parameters and reducing the number of input parameters will reduce the complexity of the problem and improve the TMC estimation by GA-SVM.