Large branchiopods are considered the flagship group for endorheic temporary wetlands globally. Large branchiopod diversity and water quality were assessed from temporary pans in the Khakhea-Bray transboundary aquifer (KBTA) region, a previously unexplored area in the North West Province, South Africa. Ten freshwater pans and a salt pan were sampled across two seasons (summer and winter) in 2022. Six large branchiopod species were identified across seasons in the temporary pans in KBTA, namely Streptocephalus namibiensis Hamer & Brendonck, 1993, Streptocephalus ovamboensis Barnard, 1924, Branchipodopsis wolfi Daday, 1908, Phallocryptus spinosa (H. Milne Edwards, 1840), Triops sp. and Ozestheria australis (Lov & eacute;n, 1847). The record of P. spinosa in the salt pan was new for North West Province and South Africa. The current data were combined with previous records, revealing that to date, 13 large branchiopod species have been documented in the North West Province. Triops sp., B. wolfi, and O. australis were recorded in summer and were the most common recorded species, whereas S. ovamboensis was only recorded in winter. Species richness was high in summer as compared to winter. The diversity of large branchiopods was mainly influenced by water temperature and phosphates in summer, sediment sodium influenced the diversity in winter. The study elevates conservation through the documentation of large branchiopods of the Khakhea-Bray transboundary aquifer region but also underscores the urgent need to prioritise the conservation of these highly sensitive ephemeral systems which sustain unique assemblages for arid landscapes across the globe.