Long-term exposure to infectious disease is thought to be one of the strongest selective pressures experienced by human populations throughout their evolutionary history, and has the potential to shape genetic diversity at immune loci. Using single-cell V(D)J sequencing we have examined the diversity of T cell receptor (TCR) sequences in approximately 200 donors from Indonesia, a tropical country with a high infectious disease burden. By comparing samples collected across two sites in the islands of Bali and New Guinea, we explore how environmental factors interact with genetic influences and shape the adaptive immune system in healthy individuals. We find that different populations within each island exhibit varying V(D)J gene usage, which may be influenced by environmental factors. Furthermore, Balinese donors exhibit TCR sequences that more closely match those in public V(D)J diversity databases, in contrast to the Papuans, which may be due to a limited representation of TCR diversity being captured by public databases, or other factors affecting TCR variation within donors. We integrate V(D)J data with gene expression data from the same cells to refine our immune cell types classification and investigate differences in V(D)J usage during T cell development. Finally, we find that sample processing time has a significant impact on data quality, which may reflect differential mortality of specific T cell subtypes, and introduces significant challenges in the interpretation of data generated in the field.