Satellite remote sensing provides an effective technical means for the precise extraction of information on aquacultural areas, which is of great significance in realizing the scientific supervision of the aquaculture industry. Existing optical remote sensing methods for the extraction of aquacultural area information mostly focus on the use of image spatial features and research on classification methods of single aquaculture patterns. Accordingly, the comprehensive utilization of a combination of spectral information and deep learning automatic recognition technology in the feature expression and discriminant extraction of aquaculture areas needs to be further explored. In this study, using Sentinel-2 remote sensing images, a method for the accurate extraction of different algae aquaculture zones combined with spectral information and deep learning technology was proposed for the characteristics of small samples, multidimensions, and complex water components in marine aquacultural areas. First, the feature expression ability of the aquaculture area target was enhanced through the calculation of the normalized difference aquaculture water index (NDAWI). Second, on this basis, the improved deep convolution generative adversarial network (DCGAN) algorithm was used to amplify the samples and create the NDAWI dataset. Finally, three semantic segmentation methods (UNet, DeepLabv3, and SegNet) were used to design models for classifying the algal aquaculture zones based on the sample amplified time series dataset and comprehensively compare the accuracy of the model classifications for achieving accurate extraction of different algal aquaculture information within the seawater aquaculture zones. The results show that the improved DCGAN amplification exhibited a better effect than the generative adversarial networks (GANs) and DCGAN under the indexes of structural similarity (SSIM) and peak signal-to-noise ratio (PSNR). The UNet classification model constructed on the basis of the improved DCGAN-amplified NDAWI dataset achieved better classification results (Lvshunkou: OA = 94.56%, kappa = 0.905; Jinzhou: OA = 94.68%, kappa = 0.913). The algorithmic model in this study provides a new method for the fine classification of marine aquaculture area information under small sample conditions.