The number of beach closings due to bacterial contamination continues to be on the 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 (E. 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 generated high R2 values (~0.8) and show promise for beach management.