The high heterogeneity of silica cycling in coastal margins and the lack of silica data (compared to nitrogen and phosphorus) prevent the estimation of global silica retention in estuaries. In this study, the spatial and temporal variability of pore water silicic acid (Si(OH)4) profiles - that integrate benthic transport and reaction processes - was investigated at different spatial (meter, longitudinal and cross-section, intra-estuary) and temporal (tidal, seasonal) scales in two macrotidal estuaries, very close geographically but differing essentially in their shape. Studying the spatial and temporal variability of Si(OH)4 concentrations in pore waters provided evidence for the importance of transport processes, e.g. bio-irrigation, tidal pumping, resuspension and any combination of these processes, in affecting Si(OH)4 concentrations and fluxes and hence, temporary or permanent retention along the land-ocean continuum. We confirm that aSiO2 transported by rivers and estuaries clearly deserves to be better characterized as it provides an important source of reactive aSiO2 to sediments. This study brings crucial information which allows to (1) deconvoluate spatial and temporal scales, although both are most often in complete interaction, (2) design the most appropriate sampling schemes to be representative of any given system and to extrapolate at the scale of the whole estuary, (3) quantify uncertainty associated to the estimations of Si(OH)4 stocks and fluxes in this type of ecosystem, essential for budget calculations. We showed that two adjacent small macrotidal estuaries, may exhibit different behaviors regarding Si retention. Temporary retention has been observed in the meanders of the Aulne Estuary and not along the more linear Elorn Estuary, demonstrating the importance of the morphology and hydrodynamism component of the estuarine filter. This effort needs to be pursued in other systems and climatic zones, but our study suggests that the typology should not only account for the different types of land-ocean continuum (fjord, delta, mangrove.), but also incorporate the physical or biological attributes of the estuarine filter.