Legionellae constitute a frequent contamination of warm water systems and can lead to serious infections. Therefore, in many countries it is mandatory to monitor warm water systems for their presence. The method of examination in Germany is regulated by guideline ISO 11731 and DIN EN ISO 11731-2, and the results are reported as concentration of Legionella spp. Only limited information is available on the presence of individual species of Legionellae in the examined systems, since most investigations and research focus solely on Legionella pneumophila as the most important human pathogen. In this study 76,220 samples obtained from 13,397 warm water systems originating from 24 different zip code districts covering an area of more than 71,000km2 in southern Germany were examined. This resulted in the identification of 47,924 Legionella isolates to the species level using a MALDI-TOF mass spectrometry-based method. Legionella species distribution was analyzed with respect to warm water system type, geographic region (defined as zip code district) and temperature during sample taking. Overall, 20.7% of the samples were found positive for Legionella species and 14 different species of Legionella were recovered. These were not equally present throughout the geographic area investigated, but instead an individual regional diversity of Legionella species was observed for the examined zip code districts. Although Legionella pneumophila represented 84% of all contaminations found, depending on the geographical region its proportion varied substantially between 57.5% and 91.2%. The occurrence of other species was also of importance since they accounted for up to 42% of contaminations regionally, with Legionella londiniensis being most prominent representing up to 38.8% of recovered colonies. In addition, the influence of temperature on the individual species was disparate, but the temperature range between 50°C and 59°C was identified as the optimal condition for facilitating emergence of the majority of recovered Legionella species. The identification of Legionella to the species level by MALDI-TOF allowed for a more concise depiction of the regional distribution and the ecology of this genus, and may be of additional value when counter measures need to be initiated.