Saline aquatic systems include inland and marine-derived lakes, solar salterns, or temporary inland saline ponds. Despite their high salinity, these ecosystems are inhabited by diverse microbial communities driving full biogeochemical cycling of main elements. To date, numerous salt-loving (or 'halophilic') environmental strains with metabolic traits of applicative interest belonging to all Domains of Life (Bacteria, Archaea, Eukarya) have been isolated from saline aquatic systems. The aim of the present work is to briefly review some of the most relevant achievements in the bioprospecting of saline aquatic systems for compounds and metabolic capabilities with potential uses in the environmental, industrial, and food biotechnologies. Additionally, the successful stories of current commercial exploitations of a few halotolerant (e.g., the bacterium Halomonas elongata), halophilic (e.g., the green algae Dunaliella sp.), and haloalkaliphilic microbes (e.g., the sulfur-oxidizing bacteria of genus Thioalkalivibrio sp.) are overviewed.