In order to avoid a bias toward highly toxic but poorly bioavailable compounds in the effect-directed analysis (EDA) of soils and sediments, approaches are discussed to consider bioavailability in EDA procedures. In parallel, complimentary approaches for making toxicity identification evaluations (TIEs) more capable of performing high resolution fractionation, toxicant isolation and identification are described. These approaches focus on three processes including bioaccessibility based on desorption kinetics from the abiotic matrix, activity driven partitioning into pore water and biota tissue or a biomimetic tool, and EDA and TIE in tissues and body fluids representing toxicological bioavailability including the toxicokinetics of the selected organism. Bioaccessibility may be addressed by extraction procedures that are designed to yield rapidly desorbing fractions including mild solvent extraction, desorption into water with subsequent adsorption to a competitive adsorbent such as TENAX^® or cyclodextrin, supercritical fluid extraction, or biomimetic extraction with gut fluids of potentially affected organisms. While equilibrium partitioning-based extraction procedures may simulate partitioning into biota quite well they often fail to provide sufficient amounts of toxicants for subsequent EDA and TIE. Partition-based dosing, which may be combined with bioaccessibility-directed extraction methods, provides an excellent tool to simulate partitioning in sediments and to provide constant and well-defined concentrations in bioassays. EDA studies in fish and mussel tissues as well as in fish bile demonstrate the potency of the identification of bioavailable toxicants in biota. Continued research on the described approaches promises to improve the usefulness of both EDA and TIE in future applications.