This thesis describes the development of a particle tracer technique for making short-term, in situ measurements of aquatic bed sediment biodiffusion coefficients. The bioturbation process in the upper sediment layers of streams, lakes, estuaries, and the marine environment moves particles and porewater. When present, organic chemicals, metals, colloids, etc., are transported across these layers and exchanges may occur at the sediment-water interface. Fickian biodiffusion coefficients that characterize such particle movements, Db (cm2/yr), are used for assessing chemical diagenesis rates and contaminant fluxes and are specific to each site. Chemical Fate and Transport (CFaT) models, developed for tracking contaminants in aquatic environments, require a method of measuring the biodiffusion coefficient at specific locations. This measurement protocol should also be able to detect seasonal or other time dependent variations in the biodiffusion coefficient for improved model predictions. Magnetite, a tracer with a long historical use in scientific studies of porous media, particle transport, etc., was chosen. Unlike most of the other tracers used in this field, magnetite, an inexpensive and naturally occurring iron oxide, is readily obtained from ceramic supply companies and gives reasonable estimations of biodiffusion coefficients from short-term experiments. The steps in the protocol include deployment and retrieval of the tracer, magnetite separation and measurement, math model interpretation, and statistical treatment of data. Application of the technique was tested on South Capitol Lake, a manmade, freshwater lake located in Baton Rouge, Louisiana. The surficial sediment in this lake was found to contain a fairly large population of oligochaete worms in abundances of approximately 18 000 worms/m2. Field deployments of magnetite were conducted in December 2001, January 2002, and February 2002, giving biodiffusion coefficient values of 0.9495 ± 0.2565 cm2/yr, 0.4566 ± 0.3314 cm2/yr, and 0.6591 ± 0.3876 cm2/yr, respectively. Although the protocol was capable of in situ measurements, testing over one or more calendar years at this and other sites will be needed to determine if the magnetite tracer protocol can be used to detect changes in Db with the seasons of the year.