Background: The Balaruc-les-Bains’ thermal mud was found to be colonized predominantly by microorganisms, with cyanobacteria constituting the primary organism in the microbial biofilm observed on the mud surface. The success of cyanobacteria in colonizing this specific ecological niche can be explained in part by their taxa-specific adaptation capacities, and also the diversity of bioactive natural products that they synthesize. This array of components has physiological and ecological properties that may be exploited for various applications. Methods: Nine cyanobacterial strains were isolated from Balaruc thermal mud and maintained in the Paris Museum Collection (PMC). Full genome sequencing was performed coupled with targeted and untargeted metabolomic analyses (HPLC-DAD and LC-MS/MS). Bioassays were performed to determine antioxidant, anti-inflammatory, and wound-healing properties. Results: Biosynthetic pathways for phycobiliproteins, scytonemin, and carotenoid pigments and 124 metabolite biosynthetic gene clusters (BGCs) were characterized. Several compounds with known antioxidant or anti-inflammatory properties, such as carotenoids, phycobilins, mycosporine-like amino acids, and aeruginosins, and other bioactive metabolites like microginins, microviridins, and anabaenolysins were identified. Secretion of the proinflammatory cytokines TNF-α, IL-1β, IL-6, and IL-8 appeared to be inhibited by crude extracts of Planktothricoides raciborskii PMC 877.14, Nostoc sp. PMC 881.14, and Pseudo-chroococcus couteii PMC 885.14. The extract of the Aliinostoc sp. PMC 882.14 strain was able to slightly enhance migration of HaCat cells that may be helpful in wound healing. Several antioxidant compounds were detected, but no significant effects on nitric oxide secretion were observed. There was no cytotoxicity on the three cell types tested, indicating that cyanobacterial extracts may have anti-inflammatory therapeutic potential without harming body cells. These data open up promising uses for these extracts and their respective molecules in drugs or thermal therapies.