The field data provide species distribution data of a freshwater invertebrate group called large branchiopods from freshwater habitats from one of the megadiverse regions of the world, Western Ghats of India. The data have been collected from 2009 until 2017 at 45 localities. Qualitative representative sampling was carried out using a hand net having a mesh size of 150 µm. A total of 12 species including three new endemic species and two distinct populations of large branchiopods were observed in the sampled localities (Schwentner et al. 2012; Rogers and Padhye 2014; Padhye and Ghate 2016; Padhye et al. 2018; Modak et al. in press). These habitat data, therefore, are important in the context of biodiversity conservation planning and management in general. Detailed metadata can be found in the Freshwater Metadatabase (http://data.freshwaterbiodiversity.eu/metadb/bf_mdb_view.php?entryID=FWM_21) and in the Freshwater Metadata Journal (http://data.freshwaterbiodiversity.eu/metadb/showfmjarticle.php?dbcode=FWM_21).