Historically, wetlands have not been given much attention in terms of their value due to the general public being unaware. Nevertheless, wetlands are still threatened by many anthropogenic activities, in addition to ongoing climate change. With these recent developments, water level prediction of wetlands has become an important task in order to identify potential environmental damage and for the sustainable management of wetlands. Therefore, this study identified a reliable neural network model by which to predict wetland water levels over the Colombo flood detention area, Sri Lanka. This is the first study conducted using machine learning techniques in wetland water level predictions in Sri Lanka. The model was developed with independent meteorological variables, including rainfall, evaporation, temperature, relative humidity, and wind speed. The water levels measurements of previous years were used as dependent variables, and the analysis was based on a seasonal timescale. Two neural network training algorithms, the Levenberg Marquardt algorithm (LM) and the Scaled Conjugate algorithm (SG), were used to model the nonlinear relationship, while the Mean Squared Error (MSE) and Coefficient of Correlation (CC) were used as the performance indices by which to understand the robustness of the model. In addition, uncertainty analysis was carried out using d-factor simulations. The performance indicators showed that the LM algorithm produced better results by which to model the wetland water level ahead of the SC algorithm, with a mean squared error of 0.0002 and a coefficient of correlation of 0.99. In addition, the computational efficiencies were excellent in the LM algorithm compared to the SC algorithm in terms of the prediction of water levels. LM showcased 3–5 epochs, whereas SC showcased 34–50 epochs of computational efficiencies for all four seasonal predictions. However, the d-factor showcased that the results were not within the cluster of uncertainty. Therefore, the overall results suggest that the Artificial Neural Network can be successfully used to predict the wetland water levels, which is immensely important in the management and conservation of the wetlands.