Climate-driven warming may enhance the spread of warm-adapted alien cyanobacteria in freshwater ecosystems. This study assessed four nostocalean cyanobacteria from European lakes—native Aphanizomenon gracile and alien Chrysosporum bergii, Raphidiopsis raciborskii, and Sphaerospermopsis aphanizomenoides—to evaluate species identity, toxin production potential, and thermal responses. A polyphasic approach combining phylogenetic analysis, morphology, and toxin screening confirmed the identifications and revealed a saxitoxin-producing A. gracile strain. No toxin genes were detected in the alien taxa. Experimental testing across 15–35 °C demonstrated broader thermal tolerance in the alien species, which maintained positive growth across 20–35 °C but showed limited performance at 15 °C. In contrast, the native Aphanizomenon gracile maintained positive growth at 15 °C, indicating greater adaptation to cooler conditions. Isolate-specific variation at thermal extremes highlighted the importance of ecotype-level traits. Our findings suggest that rising temperatures, combined with strain-level physiological diversity, may increase the risk of alien cyanobacteria establishing and forming blooms in temperate lakes. This study supports the need for monitoring strategies that integrate taxonomy, ecophysiology, and local adaptation to better assess invasion potential under changing environmental conditions.