Chlorophyll-a concentrations in coastal and inland waters is acknowledged as an important factor to estimate Water Bodies Quality Status. Remote sensing analysis is a fast, cost-effective, and reliable methodology that can be used to assess the phenological patterns of aquatic ecosystems. The purpose of this study is to assess the phenology patterns of a eutrophic water body and present a novel methodology to fill in the missing values of the daily Surface Reflectance MODIS Aqua dataset. The proposed methodology is to apply Principal Component Analysis to generate the missing values from the chlorophyll-a concentrations and better assess Water Body's Trophic Status. The pilot study is Aitoliko Lagoon, a semi-closed Greek water body with eutrophication. The analysis reveals that sampling stations of swallow waters have higher variance in chlorophyll-a concentrations, favoring the deep waters sampling pixels for evaluating the water body's trophic status. The proposed PCA methodology showed a clear phenological pattern of chlorophyll-a with algae bloom from April and high chlorophyll-a concentrations until August, which is what is expected from a eutrophic lagoon and specifically for Aitoliko lagoon.
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