<p>Acid sulfate soils (ASS) pose severe physicochemical challenges for shrimp nursing due to water-column acidification and dissolved-metal toxicity. This study evaluates amorphous biosilica derived from rice husk ash (RHA) as a robust biogeochemical regulator and phytoplankton stimulant for Pacific white shrimp (<i>Litopenaeus vannamei</i>) post-larvae. Over a 21-day nursery period conducted in hapa replicates (<i>n</i> = 4) within adjacent pond plots, water quality and biological performance were compared between RHA-biosilica treatment and control groups. Soil analysis revealed that while pre-conditioning remediation reduced iron (Fe) and aluminum (Al) levels, the pond bed retained a high latent potential acidity (S_POS 1.22%). However, RHA-biosilica successfully mitigated acid release into the water column (<i>p</i> &lt; 0.05), maintaining robust pH stability (mean &gt; 7.0) and sustained silicate concentrations &gt; 4.0&#xa0;mg/L, whereas the control units experienced wide pH fluctuations (5.5–8.0) and a significant decline in silica concentration to less than 2.0&#xa0;mg/L. Stable silica availability promoted a resilient, diatom-dominant succession (<i>Thalassiosira</i> sp. and <i>Navicula</i> sp.) that successfully suppressed unfavorable phytoplankton groups and prevented hazardous “boom-and-bust” algal crashes. This ecological stabilization maintained total ammonia nitrogen at a safe baseline of 0.02&#xa0;mg/L, significantly lower than the 1.23&#xa0;mg/L observed in the control (<i>p</i> &lt; 0.001), via a dual-action mechanism involving physicochemical adsorption and biological assimilation. While post-larval survival was high (&gt; 93%) in both groups, the RHA-biosilica treatment significantly enhanced growth, achieving a final weight of 0.165&#xa0;g (<i>p</i> = 0.011) and a 31% increase in biomass. These results indicate that RHA-biosilica is an effective regulator and circular-economy solution for transforming marginal ASS into resilient aquaculture landscapes.</p>