Natural aquatic colloids (solids with dimensions between 1 nm and 1 micron) were studied in cave waters that feed secondary carbonates [speleothems]. Results show that during hydrologically quiescent periods, trace metal (Tr) binding (e.g. Cu, Ni, Co) is dominated by humic-like, natural organic matter (NOM), with the smallest NOM-Tr complexes (≤1 to ca. 4 nm diameter) being the least labile at high pH (>pH 10). Partitioning of NOM:Tr between solution and crystal occurs minimally for the strongest complexes, providing a measure of NOM adsorption. Rapid fluxes of coarse (>100 nm) soil organic matter (SOM) and Tr in dripwaters often follow peak infiltration events, the coarse fraction of NOM quenching fluorescence in finer fractions (<100 nm). Termed ‘high-flux’ (HF), this mode of NOM-metal transport contrasts with the humic-like or ‘low-flux’ (LF) mode both hydrologically and chemically, resulting in shifts in trace metal ratios (e.g. Cu:Ni) which are characteristic of changes in the competitive binding of metals for suitable sites in NOM, and diagnostic of qualitative shifts in NOM composition (i.e. relatively more aromatic/hydrophobic). This process becomes manifest in speleothems, resulting in high- and low-flux trace metal end-members and providing information on NOM aromaticity. Changes in HF:LF metal ratios in speleothems are linked to processes in soils which are ultimately mediated by climate (i.e. ambient temperature and infiltrating precipitation); they may provide information on infiltrating precipitation, on the occurrence of surface disturbances (e.g. deforestation) and NOM composition. HF:LF indices complement the existing array of speleothem climate proxies, but each specific system and setting must be understood to ensure their proper interpretation.