Siderophores are low molecular mass organic compounds with high iron(III) stability constants. They are produced by many microorganisms, often in combination with low molecular mass organic acids (LMMOAs). Both siderophores and LMMOAs accelerate mineral weathering, thereby enhancing mineral nutrient availability. Siderophore concentrations in natural environments, however, are largely unknown. In the present work, analytical methods based on liquid chromatography (LC) electrospray ionization mass spectrometry (ESI‐MS) were developed and used for concentration determination of selected hydroxamate siderophores and LMMOAs. The use of capillary LC with on‐line pre‐concentration via column switching enabled siderophore quantification with detection limits of 0.1 ‐ 5 nM. Through solid phase extraction even lower detection limits were achieved. In Swedish podzol soil solutions concentrations up to 12 nM ferricrocin and 2 nM ferrichrome were found in the upper soil layes. Additionally, in axenic pine (Pinus sylvestris) seedling cultures, the ectomycorrhizal fungus Hebeloma crustuliniforme was shown to produce ferricrocin as the main siderophore. Moreover, ferricrocin was found in enriched Baltic Sea cyanobacterial populations at concentrations up to 1 nM, while concentrations up to 0.05 nM ferrioxamine B were determined in Baltic Sea surface waters during cyanobacterial blooms. Siderophores have strong affinities for some actinides and may affect radionuclide mobilization in deep subsurface nuclear wase repositories. Two subsurface bacterial strains were shown to produce siderophores under aerobic conditions, i.e. Pseudomonas stutzeri produced mainly ferrioxamine E and Pseudomonas fluorescens produced one pyoverdin siderophore. Siderophores produced by aerobically grown P. stutzeri were not observed either in anaerobic cultures or in deep subsurface water samples.