To understand ecosystem functioning in coastal zones it is essential to identify the main pathways and magnitude of nutrient and organic matter fluxes. The different methods that have been applied to quantify material fluxes in tropical coastal ecosystems can be categorized into two fundamentally distinct approaches: direct flux measurements (Section 12.2) and chemical tracer techniques (Section 12.3). For direct flux measurements, the bidirectional flow of water is determined and multiplied with concentrations to obtain fluxes of inorganic nutrients or organic constituents. Water discharge can be measured directly with help of current meters and gauges, or indirectly through use of water tracers. The source of nutrients and organic matter can then be identified with help of specific chemical tracers, mainly isotopes or molecular properties. A combination of tracer techniques and direct flux measurements is most powerful to obtain quantitative information on the fluxes of organic matter and nutrients from the various sources in coastal systems but has very rarely been applied. Regarding source assessments of suspended and sedimentary organic matter, a large number of molecular biomarkers are readily available (Section 12.4). For dissolved organic matter, emerging molecular fingerprinting techniques including ultra-high resolution mass spectrometry may lead to major advances in the future. © 2009 Springer Science+Business Media B.V.