While deep learning models have been extensively applied to land-use land-cover (LULC) problems, it is still a relatively new and emerging topic for separating and classifying wetland types. On the other hand, ensemble learning has demonstrated promising results in improving and boosting classification accuracy. Accordingly, this study aims to develop a classification system for mapping complex wetland areas by incorporating deep ensemble learning and satellite datasets. To this end, time series of Sentinel-1 dual-polarized Synthetic Aperture Radar (SAR) dataset, alongside Sentinel-2 multispectral imagery (MSI), are used as input data to the model. In order to increase the diversity of the extracted features, the proposed model, herein called WetNet, consists of three different submodels, comprising several recurrent and convolutional layers. Furthermore, multiple ensembling sections are added to different stages of the model to increase the transferability of the model (to other areas) and the reliability of the final results. WetNet is evaluated in a complex wetland area located in Newfoundland, Canada. Experimental results indicate that WetNet outperforms the state-of-the-art deep models (e.g., InceptionResnetV2, InceptionV3, and DenseNet121) in terms of both the classification accuracy and processing time. This makes WetNet an efficient model for large-scale wetland mapping application. The python code of the proposed WetNet model is available at the following link for the sake of reproducibility: https://colab.research.google.com/drive/1pvMOd3_tFYaMYGyHNfxqDxOiwF78lKgN?usp=sharing