Several studies have found that, since 1975 at least, the atoll lagoon of Takapoto exhibits high salinities and high planktonic chlorophyll concentrations. We used observations gathered in Takapoto and 23 other atoll lagoons between 1995 and 2000 to study the water renewal rate (determined by different approaches) of Takapoto relative to that of the other lagoons. This rate is controlled by reef rim aperture, which is abnormally low in Takapoto. Across this set of lagoons, average water residence time was correlated with salinity, and with two descriptors of water column biological properties, chlorophyll and dissolved organic matter contents. In parallel to these bulk quantitative variations, qualitative variations were found inside this trophy gradient, concerning the size of primary producers (proportion of cells > 2.7 μm) and the composition of seston (relative phosphorus content). Takapoto Lagoon fits into a gradient of water residence time that controls the overall trophic web organization.