Objective To investigate the prevalence, isolation, identification, characterization, antibiotic profile and pathogenicity of Legionellae isolated from various set of waters. Methods A total of 400 water samples were collected from different water sources. Water samples were pretreated using acid treatment followed by concentration and culture on buffered charcoal yeast extract agar. Parameters like ability of Legionella isolates to grow in various pH range, effect of different concentrations of chlorine and effect of different temperature optima were set up. Biochemical tests were performed to separate Legionellae into species. Antibiotic sensitivity tests and test for pathogenicity were also conducted on isolated strains. Results The rates of isolation of Legionella pneumophila (L. pneumophila) in different water sources were found to be 20% (lakes), 10% (ponds), 8% (water-tanks) and 1% (rivers). Most of the isolates could grow in variable pH 6–8 and it could also survive the normal level of chlorination and even at temperature of 42 °C. Isolated species of Legionellae resulted in identification of 5 different species, L. pneumophila being the dominant one. Strains of L. pneumophila were resistant to many antibiotics. Inoculation of Legionellae into intracerebral route of suckling mice revealed that L. pneumophila was the most virulent. Conclusions Serious and fatal L. pneumophila infections may be transmitted through water. Legionella can survive under various conditions in various water sources. L. pneumophila is the important pathogen causing human disease. Great challenge prevails to health care professionals because these Legionellae acquired antibiotic resistance to many routinely prescribed antibiotics.