Wastewater Treatment Pond (WTP) is an effective remediation technology for economically developing nations. Although it's excessive organic and nutrient loads with higher water logging time triggers mixed and unprofitable microalgal mats. This may serve as a seeding source for Cyanobacterial bloom in receiving waterbodies. Since, to maintain the growth of desirable algal species in WTPs, understanding towards environmental regulation and algal mat composition is important, especially for tropical countries, like India. In this study, biological treatment pond (BTP) and outlet pond (OP), of a tannery effluent treatment plant in eastern coast of India, were chosen for surveying the algal community composition concerning ecological parameters. Nearly, both the ponds were polluted, but the diversity was lower in BTP due to its elevated nutrient content (Ammonia 173 mg L−1) and higher persistent organic matters (COD 301.7 mg L−1) than OP. Using canonical correspondence analysis, seasonal variations showed higher species abundance during early summer compared to other seasons. A total of 37 taxa forming thick algal mats were recorded. The matrix of mats was mainly composed of Cyanobacterial members such as Phormidium, Leptolyngbya, Spirulina, and Pseudanabaena, followed by diatoms, especially Amphora and Nitzschia. Diatoms commonly occurred as embedded component in the entangled matrix of blue-green algal filaments. Hierarchical cluster analysis was employed to group all these taxa based on their seasonal appearance and abundance. This year-long intensive study revealing seasonal algal mat composition patterns in these WTPs will ultimately safeguard the livelihood and security of adjoining localities through proper site-specific pollution control. © 2021, The Author(s), under exclusive licence to Springer Nature Switzerland AG.