In recent years, reaction transport models have gained importance in the study of diagenesis, which describes the chemical, biological and physical processes that take place in sediments. This project reports on factors influencing chemical profiles in lake sediments through an exploration of a generic reaction transport model which includes representations of the major reactions involved in the cycling of iron, sulfur and phosphorus. We have performed a global sensitivity analysis examining the steady state effects of physical, kinetic and thermodynamic factors on the magnitude, shape and burial concentrations of chemical profiles of iron, sulfur and phosphorus-bearing species. The environmental conditions were varied within a broad range typical of lake sediments. The exploration demonstrates the importance of the nature of boundary conditions (i.e. characteristics of the water column) and their coupling to the water column dynamics. The study additionally points to some chemical mechanisms such as precipitation of vivianite and scavenging of vivianite by sulfide having a dominant influence on the depth profiles of chemical species. Investigation also shows the importance of physical transport processes such as bioturbation near the sediment water interface and sedimentation velocity. Additionally, the distribution of reaction rates with depth and their role in shaping the profiles of chemical concentrations under typical environmental conditions were investigated