Declining macrophytes in eutrophic lakes are altering material cycling in sediments. However, the transformation of arsenic (As) in response to these changes remains poorly understood. In this study, high-resolution dialysis was used to measure dissolved As in sediments from macrophyte-dominated (MD) and algae-dominated (AD) zones across different seasons. The relationship between sedimentary As fractionation and environmental variations was analyzed, and the As transformation process was explored. Results showed that the shift from macrophyte- to algae-dominated zones enhanced As release in sediments. Dissolved As in pore water of AD peaked at 120.36 μg/L in summer, exhibiting the highest release intensity, while MD showed a notable As release profile in spring (34.92 μg/L). In spring, decomposition and acidification of macrophyte residues, along with organic matter (OM) complexation, promoted the release of adsorbed As in MD. In contrast, reduction and dissolution of iron (Fe) oxides, along with competition for adsorption sites by dissolved phosphorus (P), drove As release in AD during summer. The high humification and low redox potential in MD sediments in summer promoted As-S co-precipitation, leading to As sequestration instead of release, this contrasts with the common view that warmer temperatures favor As release from sediments. The conversion from macrophytes to algae in eutrophic lakes may exacerbate the risk of As release, warranting further investigation.