<p>In response to the global demand for high-quality protein, <i>Litopenaeus vannamei</i> aquaculture has rapidly expanded. However, microalgal blooms often degrade water quality, resulting in reduced yields and significant financial losses. This study investigated the recovery dynamics of substrate microalgae, which act as seed banks for microalgal blooms, and identified early warning thresholds for algae under varying environmental conditions. Sediments from bfIGuccess (BS) and breeding failure (BF) sheds were analyzed to evaluate the effects of temperature (6&#xa0;°C–21&#xa0;°C), light intensity (50–2,000&#xa0;lx), and nutrient types (BG11 and raw water). The findings indicated that environmental factors influencing microalgal recovery followed the priority order: temperature &gt; light &gt; nutrient salts. The highest recovery was observed at temperatures of 11&#xa0;°C and 16&#xa0;°C under 2,000&#xa0;lx illumination. Key early warning algal species, including <i>Melosira granulata</i>, <i>Cyclotella</i>, and <i>Chlorella</i>, exhibited thresholds of 0.9–42.9 × 10⁴ cells/g, 0.1–28.8 × 10⁴ cells/g, and 1.0–31.7 × 10⁴ cells/g, respectively. This study uniquely linked substrate algae recovery to aquaculture failures, providing quantitative thresholds and actionable insights for proactive microalgal blooms monitoring and control. These findings form a scientific basis for improving water quality management and ensuring sustainable <i>L. vannamei</i> aquaculture</p>