<p>Bedrock composition, in particular the proportion of carbonate, can influence the dissolved inorganic carbon concentration and also the carbonate chemistry of rivers, but its effects on the nitrogen cycle in rivers are usually overlooked. Here we present geochemical composition measurements of rivers across the Pearl River Basin in China that show that dissolved organic nitrogen (DON) is positively correlated with dissolved inorganic nitrogen and follows the variation in solar radiation in the carbonate-dominated region during the wet season, but not in the non-carbonate-dominated region. In situ incubations show that organic nitrogen production is strengthened in the regions with high dissolved inorganic carbon and high temperature and solar radiation. DON zonation in the dry season is not obvious owing to the limitation of low temperature on nitrogen assimilation. We also report a similar DON contrast in carbonate-dominated and non-carbonate-dominated regions in Malang in Indonesia. Furthermore, from an analysis of global published data, we find that a modified Michaelis–Menten model incorporating carbon limitation provides a much better fit to the global latitudinal distribution of DON globally. Hence, we propose that carbonate weathering enhancement of organic nitrogen production occurs ubiquitously.</p>