The retrieval of chlorophyll-a (Chl-a) concentrations relies on empirical or analytical analyses, which generally experience difficulties from the diversity of inland waters in statistical analyses and the complexity of radiative transfer equations in analytical analyses, respectively. Previous studies proposed the utilization of artificial neural networks (ANNs) to alleviate these problems. However, ANNs do not consider the problem of insufficient in situ samples during model training, and they do not fully utilize the spatial and spectral information of remote sensing images in neural networks. In this study, a two-stage training is introduced to address the problem regarding sample insufficiency. The neural network is pretrained using the samples derived from an existing Chl-a concentration model in the first stage, and the pretrained model is refined with in situ samples in the second stage. A novel convolutional neural network for Chl-a concentration retrieval called WaterNet is proposed which utilizes both spectral and spatial information of remote sensing images. In addition, an end-to-end structure that integrates feature extraction, band expansion, and Chl-a estimation into the neural network leads to an efficient and effective Chl-a concentration retrieval. In experiments, Sentinel-3 images with the same acquisition days of in situ measurements over Laguna Lake in the Philippines were used to train and evaluate WaterNet. The quantitative analyses show that the two-stage training is more likely than the one-stage training to reach the global optimum in the optimization, and WaterNet with two-stage training outperforms, in terms of estimation accuracy, related ANN-based and band-combination-based Chl-a concentration models.

Chlorophyll-a (Chl-a) concentration, a crucial indicator of phytoplankton biomass, is sensitive to seasonality. The variations in trophic states regarding seasonality and the changes of spectral properties of water bodies pose uncertainties to the accuracy of remote sensing semiempirical models. In particular, lakes in subtropical regions generally experience different trophic states in dry and wet seasons. In this study, a season-insensitive Chl-a retrieval model using multitask convolution neural network with multiple output layers (MCNN) is proposed. A layer-sharing network combined with data augmentation is adopted to alleviate the issue of insufficient quantity of in situ samples. In addition, a hyperparameter optimization is performed to automatically refine the MCNN architecture. To evaluate the accuracy of proposed method, Laguna Lake, one of the largest lakes in Southeast Asia, is selected as the validation target. The lake is characterized by oligotrophic and mesotrophic states in wet season, whereas the states change to mesotrophic and low-level eutrophic states in dry season. A collection of Sentinel-3 Ocean and Land Colour Instrument Level-2 images and 409 in situ samples with the Chl-a concentration range 1.24–22.30 mg $\cdot$ m $^{-3}$ were used for model calibration and evaluation. Experimental results showed that MCNN with the performance of average $\boldsymbol{R^{2}}$ = 0.74, RMSE = 2.06 mg $\cdot$ m $^{-3}$ , Pearson's $\boldsymbol {r}$ = 0.86 outperforms related semiempirical models, including normalized difference chlorophyll index, two-band and three-band models, and WaterNet. The Chl-a prediction accuracy was improved by 7.19–14.6%, in terms of RMSE, compared with WaterNet.