For floristic study on diatoms from the source of Han and Nakdong Rivers, we collected samples in February, April, and July 2016 from Geomryongso and Neodeolsam Ponds, South Korea. Geomryongso and Neodeolsam Ponds are sources of Han and Nakdong Rivers, respectively. Thirty-eight infrageneric taxa of freshwater diatoms were identified in the collected samples from study areas. The diatom species were classified into 25 genera, 17 families, 10 orders, 5 subclasses, and 2 classes based on the taxonomic system proposed by Round et al. (1990). Nine diatom taxa—Achnanthes sinaensis, Achnanthidium atomus, Edtheriotia guizhoiana, Fragilaria recapitellata, Gyrosigma procerum, Navicula nipponica, Pinnularia pseudotabellaria, Pinnularia rabenhorstii, and Platessa barhlsii—were newly recorded, whose taxonomic features have been described; they are indicated by asterisk. We presented the taxonomic information, including the systematics, and dimension in the source of two major rivers in Korea. This study might contribute to the understanding of diversity and flora of diatoms in various freshwater environments in Korea.