The study of attached algae communities assembly mechanisms is essential for understanding the restoration of river ecosystem structure and function. This study analyzed attached algae communities in three representative rivers flowing through Guangzhou—Chebei River (natural habitat), Liede River (highly canalized), and Shahe River (mixed habitat)—that are subject to a low water level operation strategy. The analysis covered four consecutive flood seasons from 2020 to 2023, focusing on the recovery and environmental drivers of these communities under near-natural restoration measures. The results show that a total of 193 algal species across 6 phyla, 53 families, and 90 genera were recorded, with Bacillariophyta being dominant (51.26%). No significant spatial differences (P>0.05) in algal standing stock were found, while significant annual differences (P<0.001) occurred, indicating higher temporal than spatial heterogeneity. Chebei river had the highest total number of species (184), while Liede river showed the highest abundance (2.47×109 cells/m2) (3.16×103 mg/m2), Shannon Diversity Index (3.14), and Evenness Index (0.66). Annually, Liede river had the largest increases in number of species and Shannon Diversity Index (41.43%, and 15.58%, respectively), and Shahe river had the highest abundance and biomass increase (92.62%, and 96.53% respectively), with Evenness Index remaining stable at around 0.6.These findings highlight the effectiveness of near-natural restoration for attached algae recovery. Niche analysis revealed a collaborative community structure with efficient resource use and low competition. The standardized random rate analysis revealed that deterministic and stochastic processes both play dominant roles during restoration. Environmental heterogeneity impacts the relative dominance of these two processes. Redundancy analysis indicated that TN, TP, DO, water depth, and flow velocity are key factors affecting the recovery of rivers attached algae communities. The research results provide empirical support and a scientific basis for the effectiveness of near-natural restoration in urban river channels.