Random Tree (RT) and Iterative Classifier Optimizer (ICO) based on Alternating Model Tree (AMT) regressor machine learning (ML) algorithms coupled with Bagging (BA) or Additive Regression (AR) hybrid algorithms were applied to forecasting multistep ahead (up to three months) Lake Superior and Lake Michigan water level (WL). Partial autocorrelation (PACF) of each lake’s WL time series estimated the most important lag times — up to five months in both lakes — as potential inputs. The WL time series data was partitioned into training (from 1918 to 1988) and testing (from 1989 to 2018) for model building and evaluation, respectively. Developed algorithms were validated through statistically and visually based metric using testing data. Although both hybrid ensemble algorithms improved individual ML algorithms’ performance, the BA algorithm outperformed the AR algorithm. As a novel model in forecasting problems, the ICO algorithm was shown to have great potential in generating robust multistep lake WL forecasts.