The sediments of aquatic systems are host to the dynamic interplay between multiple biogeochemical cycles. Understanding these cycles relies on obtaining accurate measurements of pore water solutes at relevant spatial scales. Conventional methods, which typically rely on coring and pore water extraction by squeezing or centrifugation, do not often fully meet these requirements. Passive sampling methods such as diffusive gradients in thin films (DGT) and diffusive equilibration in thin films (DET) can provide more accurate measurements of pore water solutes at high resolution, in one or two dimensions - this approach is effective in dealing with the confounding effects of sediment heterogeneity that often occur in sediments on fine spatial scales. Here I will provide an overview of currently available gel-based passive sampling techniques, and present various examples of the application of these methods to investigating the biogeochemistry of major, minor and trace elements in aquatic sediments. These examples range from the study of iron and sulfide in marine sediments to the measurement of arsenic and antimony speciation in the freshwater sediments of a contaminated wetland. I will also discuss what the future holds for these gel-based techniques, and how they might be combined with complementary chemical imaging techniques (e.g. planar optodes) to expand our tool-box for investigating sediment biogeochemistry.