Sediment-water interactions play an important role in influencing the water quality of aquatic systems. Water quality management of freshwater systems needs to take into account this behaviour, which depends largely on early diagenetic processes that condition the physical and biogeochemical properties of the sediment. Among these processes, the redox transformations resulting from the oxidation of organic matter by the microbial activity have a major influence on the biogeochemical properties of sediments. In particular, these reactions condition the vertical profiles of nutrient concentrations, pH and metals along the sedimentary column. This paper presents a method which couples both experimental and modelling approaches in order to characterise and analyse the biogeochemistry of freshwater sediments. The modelling approach is based on a coupling between biogeochemical processes and interstitial diffusion. As pore water pH influences the behaviour of the biogeochemical species, we have extended these models to allow for the calculation of pH by taking into account the inventory of protons consumed or produced by different biogeochemical reactions. In parallel, an analytical protocol has been developed to obtain vertical distributions of the main physicochemical parameters in natural sediments cores. To illustrate this approach, we apply our method to sediments cores sampled in the Durance, a river in the south-east of France.