Tropical rivers constitute a major portion of the global aquatic C flux entering the ocean, and the Rio Negro is one of the largest single C exporters with a particularly high export of terrestrial C. We investigated the role of whitesand ecosystems (WSEs) in blackwater formation in the Rio Negro basin to develop novel constraints for the terrestrial carbon export from land to the aquatic continuum. To this end, we used ultrahigh resolution mass spectrometry (FT-MS, Orbitrap) to identify markers in dissolved organic carbon (DOC) from ground- and surface waters of two contrasting WSEs feeding Rio Negro tributaries, and compared them with known Rio Negro marker from two openly available FT-MS datasets. Tributaries were fed by a whitesand riparian valley connected to terra firme plateau, and a typical upland whitesand Campina. WSE-DOC molecular composition differed by 80% from plateau DOC, which was characterized by reworked, highly unsaturated N- and S-containing molecules. WSE-DOC contained mainly condensed aromatics and polyphenols. WSE samples differed by 10% in molecular DOC composition and also by their isotopic content (14C, 18O, 2H). Upland WSE-DOC was exported by fresh precipitation and had maximum age of 13 years, being five years older than riparian valley WSE-DOC. Unexpectedly, only markers from the upland WSE, which cover a small proportion of the landscape, were identical to Negro markers. Markers of the riparian valley WSE, which are widespread and known for high DOC export, surprisingly showed lower coverage with Negro markers. Analysis of robust matching WSE markers between FT-MS datasets by Pubchem suggested well-known plant metabolites (chromenes and benzofurans) as promising candidates for targeted approaches and calibration. Our results suggest that terrestrial DOC from upland WSEs is a main source of specific blackwater molecules missing in the regional ecosystem C balance, whereas C export from the riparian valley and especially from terra firme plateaus represents mainly recycled and transformed carbon not directly affecting the ecosystem C balance. Our study highlights the potential of high-resolution techniques to constrain carbon balances of ecosystems and landscapes. Comparisons of FT-MS datasets and complementary isotopic information shows high potential to identify robust molecular markers that link forests, soils, aquifers and aquatic systems, and are needed for a deeper understanding of the regional C cycle in tropical blackwater catchments.