In the current study, the toxicokinetics of pyrene in Daphnia magna was determined in detail, and the role of dissolved organic matter (DOM) in these processes was investigated. Uptake, biotransformation, parent compound and metabolite elimination rates (k(u), k(m), k(ep), k(em)), depuration rates, bioconcentration factors (BCFs), and biological half-lives were studied in one natural humic water, in two waters made from DOM isolates, and in DOM-free artificial fresh water. The daphnids were exposed to pyrene for 24 h and depurated for another 24 h. To analyze the data, the two-compartment model was used to obtain toxicokinetic parameters, and the depuration data were analyzed by linear regression. Extensive biotransformation of pyrene resulted in high metabolite concentration in the organisms (83% of total radioactivity) after 24 h exposure. Depuration of the parent compound seemed to be biphasic: at first, depuration was rapid, but after 4 to 10 h in uncontaminated water, the disappearance rate came close to zero. After a 24-h depuration time, 7.8% of the pyrene accumulated remained in the organism. Overall, the elimination of parent compound was faster than the elimination of metabolites, which might imply inefficient excretion of water-soluble biotransformation products from daphnids. The effect of DOM on accumulation of pyrene was seen in a decreased uptake rate, indicating lower bioavailability of the compound in waters that contain high-aromaticity DOM. In the same waters, DOM significantly accelerated pyrene biotransformation and overall elimination. Altogether, DOM appears to be able to affect toxicokinetics through mechanisms that are connected to interaction with the contaminant but also directly through interaction with biotransformation systems.