In recent years, the sediment compartment has gained more attention when performing toxicity tests, with a growing emphasis on gaining more ecological relevance in testing. Though many standard guidelines recommend using artificially formulated sediment, most sediment studies are using natural sediment collected in the field. Although the use of natural field‐collected sediment contributes to more environmentally realistic exposure scenarios and higher well‐being for sediment‐dwelling organisms, it lowers comparability and reproducibility among studies as a result of, for example, differences in the base sediment depending on sampling site, background contamination, particle size distribution, or organic matter content. The aim of this methodology contribution is to present and discuss best practices related to collecting, handling, describing, and applying natural field‐collected sediment in ecotoxicological testing. We propose six recommendations: (1) natural sediment should be collected at a well‐studied site, historically and by laboratory analysis; (2) larger quantities of sediment should be collected and stored prior to initiation of an experiment to ensure a uniform sediment base; (3) any sediment used in ecotoxicological testing should be characterized, at the very least, for its water content, organic matter content, pH, and particle size distribution; (4) select spiking method, equilibration time, and experimental setup based on the properties of the contaminant and the research question; (5) include control‐, treated similarly to the spiked sediment, and solvent control sediment when appropriate; and (6) quantify experimental exposure concentrations in the overlying water, porewater (if applicable), and bulk sediment at least at the beginning and the end of each experiment. Environ Toxicol Chem 2023;00:1–10. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.