Growth form controls the seasonal stability of nutrient-pollution mitigation by submerged macrophytes in shallow lakes.

Submerged macrophyte restoration is widely used to mitigate nutrient pollution in eutrophic shallow lakes, yet its effectiveness is often evaluated during peak plant growth rather than across the full growing season. This creates uncertainty about whether restored clear-water conditions can persist during late-season plant decline. Here, a mesocosm experiment compared a canopy-forming species, Hydrilla verticillata, with a rosette-forming species, Vallisneria natans, at vigorous- and late-growth stages. We measured overlying-water quality, sediment properties, extracellular enzyme activities, microbial community structure and metagenomic functional potential, and evaluated association patterns using Mantel analysis and partial least squares path modeling. Both species reduced nitrogen and chlorophyll-a during vigorous growth, indicating comparable short-term restoration effects. By late growth, however, H. verticillata showed biomass decline and rebound of total phosphorus and chlorophyll-a to levels similar to the unvegetated control, whereas V. natans maintained lower nutrient concentrations, stronger rhizosphere redox status and more persistent water-quality improvement. Under the shared seasonal background, this late-season divergence is more consistent with differences in growth-form strategy and late-stage plant condition than with seasonal forcing alone, and in H. verticillata may reflect senescence- and decomposition-associated nutrient rerelease. Sediment and metagenomic patterns indicated treatment- and niche-related differences in microbial functional potential for nitrogen and phosphorus cycling, although these abundance-based patterns should not be interpreted as direct process rates. The results show that submerged macrophyte restoration in nutrient-polluted shallow lakes should be assessed by full-season stability rather than peak-growth performance alone. Rosette-forming macrophytes may provide more reliable support for internal nutrient loading control where late-season persistence is a management priority.