Accurate monitoring and assessment of the environmental state, as a prerequisite for improved action, is valuable and necessary because of the growing number of environmental problems that have harmful effects on natural systems and human society. This study developed an integrated novel framework containing three modules remote sensing technology (RST), cruise monitoring technology (CMT), and deep learning to achieve a robust performance for environmental monitoring and the subsequent assessment. The deep neural network (DNN), a type of deep learning, can adapt and take advantage of the big data platform effectively provided by RST and CMT to obtain more accurate and improved monitoring results. It was proved by our case study in the Qingcaosha Reservoir (QCSR) that DNN showed a more robust performance (R2 = 0.89 for pH, R2 = 0.77 for DO, R2 = 0.86 for conductivity, and R2 = 0.95 for backscattered particles) compared to the traditional machine learning, including multiple linear regression, support vector regression, and random forest regression. Based on the monitoring results, the water quality assessment of QCSR was achieved by applying a deep learning algorithm called improved deep embedding clustering. Deep clustering analysis enables the scientific delineation of joint control regions and determines the characteristic factors of each area. This study presents the high value of the framework with a core of big data mining for environmental monitoring and follow-up assessment in a manner of high frequency, multidimensionality, and deep hierarchy.