The number of beach closings caused by bacterial contamination has continued to rise in recent years, putting beachgoers at risk of exposure to contaminated water. Current approaches predict levels of indicator bacteria using regression models containing a number of explanatory variables. Data-based modeling approaches can supplement routine monitoring data and provide highly accurate short-term forecasts of beach water quality. In this paper, we apply the nonlinear autoregressive network with exogenous inputs (NARX) method with explanatory variables to predict Escherichia coli concentrations at four Lake Michigan beach sites. We also apply the nonlinear input–output network (NIO) and nonlinear autoregressive neural network (NAR) methods in addition to a hybrid wavelet-NAR (WA-NAR) model and demonstrate their application. All models were tested using 3 months of observed data. Results revealed that the NARX models provided the best performance and that the WA-NAR model, which requires no explanatory variables, outperformed the NIO and NAR models; therefore, the WA-NAR model is suitable for application to data scarce regions. The models proposed in this paper were evaluated using multiple performance metrics, including sensitivity and specificity measures, and produced results comparable or superior to those of previous mechanistic and statistical models developed for the same beach sites. The relatively high R² values between data and the NARX models (R² values of ∼0.8 for the beach sites and ∼0.9 for the river site) indicate that the new class of models shows promise for beach management.