The dialysis porewater sampler, type Hesslein, allows sampling of sediment interstitial water according to a continuous gradient between sediment and the water column. Its equilibration time fluctuates according to the nature of sediment, so it has to be measured in each kind of sediment. The aim of this work is to develop a physical diffusion model in order to determine an equilibration time without using extensive field experiments. The model is validated by real nutrient concentration profiles obtained on two estuaries under different climates, moderate climate (estuary of the Seine) and tropical dry climate (estuary of Somone, Senegal). The results highlight that the equilibration of the dialysis porewater sampler is not homogeneous over the full sediment height investigated. Other sediment characteristics as compaction, rate of bioturbation or bacterial density must be taken into account in order to find a well-calculated value of the equilibration time.