In recent years, the key environmental importance of natural, healthy riparian ecosystems and soils has been recognized and restoration of degraded lands towards their former natural state has become an area of active research worldwide. Land use changes and restoration practices are known to affect both soil nutrient dynamics as well as nutrient transport to neighbouring areas. Microbiological transformations of the soil organic matter, including decomposition and nutrient turnover, are controlled to a large extent by soil water content, which is in turn influenced by climatic and environmental conditions such as precipitation and evapo-transpiration. In this context a novel mechanistic model to simulate water flow in the unsaturated zone, the dynamics of the soil microbial populations, carbon and nitrogen transport and turnover was developed. The mathematical model was based on a number of simplifying assumptions that will be discussed in detail in order to highlight its strengths and weaknesses and to identify the soil processes that require further research and understanding. The model was applied to analyse nutrient cycling and buffering capacity of the RECORD field site (Thur river, Thurgau canton, Switzerland), a riparian area undergoing restoration. Comparison of experimental data and simulation results in order to calibrate and validate the model is a difficult but crucial – and often overlooked – task. The strategies that were devised and applied to this case study will be presented. Based on the experience gained some ideas to facilitate such comparisons in the future will be presented. The dynamics of carbon and nitrogen at different time scales was analysed, as well as the effect of changing environmental conditions. These include the occurrence and amount of precipitation, the type of vegetation and river dynamics. Based on modelling results we concluded that soil organic matter and nutrient pools fluctuate in response to environmental forcing factors over a range time scales, from one day to one century. In other words, soil composition and functioning do not always respond rapidly to changes in external factors, a crucial aspect that should always be considered while designing river revitalization projects.