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In estuary areas, meteorological conditions have become unstable under the continuous effects of climate change, and the ecological backgrounds of such areas have strongly been influenced by anthropic activities. Consequently, the water quality of these areas is obviously affected. In this research, we identified periods of fluctuation of the general meteorological conditions in the Yangtze River Estuary using a wavelet analysis. Additionally, we performed a spatiotemporal evaluation of the water quality in the fluctuating period by using remote sensing modeling. Then, we explored how the fluctuating meteorological factors affect the distribution of total suspended solids (TSS) and chlorophyll-a (Chla) concentration. (1) The results show that from 2000 to 2015, temperature did not present significant fluctuations, while wind speed (WS) and precipitation (PR) presented the same fluctuation period from January 2012 to December 2012. (2) Based on the measured water sample data associated with Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, we developed a water quality algorithm and depicted the TSS and Chla concentrations within the WS and PR fluctuating period. (3) We found that the TSS concentration decreased with distance from the shore, while the Chla concentration showed an initially decreasing trend followed by an increasing trend; moreover, these two water quality parameters presented different inter-annual variations. Then, we discussed the correlation between the changes in the TSS and Chla concentrations and the WS and PR variables. The contribution of this research is reflected in two aspects: 1. variations in water quality parameters over a wide range of water bodies can be evaluated based on MODIS data; 2. data from different time periods showed that the fluctuations of meteorological elements had different impacts on water bodies based on the distance from the shore. The results provide new insights for the management of estuary water environments.