Whiteleg shrimp (Litopenaeus vannamei) farming is a major activity in the coastal areas of many tropical countries. To meet the demand in this market, the culture system has expanded using intensive technology, which has resulted in the emission of effluents that threaten the surrounding aquatic ecosystem. Therefore, proper aquaculture management is needed to ensure both economic and ecological benefits. This led to the emergence of eco-green aquaculture. Water quality monitoring is a critical part of aquaculture management and when performed regularly, it yields a large and complex dataset. In this study, the authors aimed to analyse the dynamics of water quality characteristics and the relationships between these variables in whiteleg shrimp ponds in a tropical eco-green aquaculture system from 2020 to 2022. Since the data includes nine parameters and is quite complex, the principal component analysis (PCA) approach was used. This method enables to identify the factors that determine water quality, which will help ensure effective and efficient aquaculture management. Consequently, the water quality variables in the studied area were reduced to five dimensions and salinity, ammonia, and pH were found to be the key factors responsible for the changes in water quality characteristics. Hence, these variables should be the focus of farming management systems.