Acid sulfate soils pose ongoing obstacles in sustainable aquaculture, primarily due to their high acidity and elevated levels of toxic metals that deteriorate water quality. This study investigated the potential of bio-silica fertilization and soil remediation to improve soil and water conditions and promote plankton growth in such acidic environments. A factorial experimental design was used to evaluate both individual and combined effects of these interventions on water quality parameters and plankton diversity. Parameters were systematically monitored, including pH, toxic metal concentrations, and nutrient availability. Data were analyzed using Analysis of Variance (ANOVA), with significant differences among treatments determined at p < 0.05 using Duncan's Multiple Range Test. Pearson’s correlation analysis was employed to examine relationships among soil and water quality, while hierarchical clustering was performed to classify plankton species based on abundance profiles. Results demonstrated that the integrated application of bio-silica and soil remediation significantly increased soil pH, reduced toxic metal levels, and enhanced nutrient bioavailability. These improvements contributed to better water quality and higher plankton abundance. In particular, the growth of diatom species such as Nitzschia sp. and Skeletonema sp. played a crucial role in supporting zooplankton populations and fostering ecosystem stability. Correlation analysis and hierarchical clustering confirmed the differential responses of plankton functional groups, with diatoms emerging as key bioindicators of treatment efficacy. The study concludes that the combination of bio-silica fertilization and soil remediation offers a promising, sustainable strategy for restoring aquaculture systems impacted by acid sulfate soils. Further research is recommended to explore the long-term ecological effects of these methods across different aquaculture environments.