This study investigates the development of algal communities and their spatiotemporal variability along the along the southern coast of the Caspian Sea (Lankaran, Astara, Masalli, and Neftchala) in 2023–2024. The study identified 75 taxa including Bacillariophyta, Chlorophyta, Cyanobacteria, Rhodophyta, Charophyta, and Ochrophyta. Results varied by location and year, with the highest values observed in Lankaran (2023) and Astara (2024). Diatoms and chlorophytes were the major dominant groups in all study areas. The Shannon diversity index ranged from 3.94 to 4.42, indicating high species richness and ecological stability of the algal communities, while the Evenness index (0.944–1.03) suggests a relatively uniform distribution of individuals among species and the absence of strong dominance. Algal communities in the study areas exhibited high species richness and ecological stability. Cluster analysis revealed that algal community structure exhibited high similarity within the same seasons and significant differences between seasons, indicating that temporal variations in abundance are mainly driven by seasonal environmental factors. Water temperature showed significant variability (8.1–27.4 °C; P < 0.0002), but no statistically significant differences were observed in parameters such as pH, and TDS (P > 0.05). The increase in temperature indicates a potential risk for algal blooms. The taxonomic composition and abundance patterns of algal communities along the southern Caspian Sea coast are influenced by environmental conditions and play an important role in evaluating the ecological health of aquatic ecosystems.