The global silicon (Si) cycle is of fundamental importance for the global carbon cycle. Diatom growth in the oceans is a major sequestration pathway for carbon on a global scale (often referred to as the biological pump). Patterns of diatoms preserved in marine sediment records can reveal both natural and anthropogenic driven environmental change, which can be used to understand silicon dynamics and climate change. Si isotopes have been shown to have great potential in order to understand the Si cycle by revealing both past and present patterns of dissolved Si (DSi) utilization, primarily when diatoms form their siliceous frustules (noted as biogenic silica, BSi). However, studies using Si isotopes are still scarce and only a few studies exist where stable Si isotopes are used to investigate the biogeochemical Si cycle in aquatic systems. Therefore, this thesis focuses on developing analytical methods for studying BSi and DSi and also provides tools to understand the observed Si isotope distribution, which may help to understand impacts of climate change and human perturbations on marine ecosystems. The Baltic Sea, one of the biggest estuarine systems in the world, was chosen as the study site. BSi samples from a sediment core in Bothnian Bay, the most northern tip of the Baltic Sea, and diatom samples from the Oder River, draining into the southern Baltic Sea were measured and reported in Paper II and III, after establishing a method for Si isotope measurements (Paper I). Si isotope fractionation during diatom production and dissolution was also investigated in a laboratory-controlled experiment (Paper IV) to validate the observations from the field. The major result is that Si isotope signatures in BSi can be used as an historical archive for diatom growth and also related to changes in climate variables. There is isotopic evidence that the Si cycle has been significantly altered in the Baltic Sea catchment by human activities. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>