Aquatic-based processes have not been well studied in tidal freshwater habitats even though they arediverse and highly variable systems. This chapter aims at a synthesis of the state of knowledge about aquaticprimary production in tidal freshwater ecosystems and the main factors that control this process. Suspendedmatter is important in tidal freshwater habitats and it is affected by estuarine processes as well as land use andriver discharge into the tidal freshwater zone from the catchment area. As a result, variation in the amount andquality of suspended matter influences the variability of light availability. The retention and transformationof nitrogen and phosphorus in the tidal freshwater zone is often intense and wetland vegetation has a majorimpact on the silica cycle within the tidal freshwater zone of estuaries. Although the primary producers follow aconstantly changing equilibrium that is influenced by tide action and river discharge, they show characteristicsthat contrast with general ideas about primary producers in estuaries. The scarceness of data, together withweaknesses in methodology to measure or model primary production, is however in striking contrast with thecomplexity and importance of these neglected ecosystems. Nevertheless, within the tidal freshwater zone of theScheldt estuary, two types of phytoplankton communities have been recorded, indicating that a typology forfreshwater tidal systems is waiting to be revealed, taking into account e.g. residence time. The dynamic natureof tidal freshwater habitats implies that static, site-bound legislative protection measures tend to be less efficientthan a functional approach. Comparative estuarine research offers a good opportunity to expand our knowledgeabout the ecological functioning of these important estuarine systems. As an example it is demonstrated here that it is possible to estimate historic suspended matter concentrations.