The surface areas of lakes alter constantly due to many factors such as climate change, land use policies, and human interventions, and their surface areas tend to decrease. It is necessary for obtain baseline datasets such as surface areas and boundaries of water bodies with high accuracy, effectively, economically, and practically by using satellite images in terms of management and planning of lakes. Extracting surface areas of water bodies using image classification algorithms and high-resolution RGB satellite images and evaluating the effectiveness of different image classification algorithms have become an important research domain. In this experimental study, eight different machine learning-based classification approaches, namely, k-nearest neighborhood (kNN), subspaced kNN, support vector machines (SVMs), random forest (RF), bagged tree (BT), Naive Bayes (NB), and linear discriminant (LD), have been utilized to extract the surface areas of lakes. Lastly, autoencoder (AE) classification algorithm was applied, and the effectiveness of all those algorithms was compared. Experimental studies were carried out on three different lakes (Hazar Lake, Salda Lake, Manyas Lake) using high-resolution Turkish RASAT RGB satellite images. The results indicated that AE algorithm obtained the highest accuracy values in both quantitative and qualitative analyses. Another important aspect of this study is that Structural Similarity Index (SSIM) and Universal Image Quality Index (UIQI) metrics that can evaluate close to human perception are used for comparison. With this application, it has been shown that overall accuracy calculated from test data may be inadequate in some cases by using SSIM, UIQI, mean squared error (MSE), peak signal to noise ratio (PSNR), and Cohen's KAPPA metrics. In the last application, the robustness of AE was examined with boxplots.