In the receiving areas of effluents from municipal wastewater treatment plants (WWTPs), aquatic organisms are threatened by adverse effects due to exposure to pharmaceutical residues. To elucidate the uptake of pharmaceuticals in fish, measurements were made in bile of brown trout (Salmo trutta) exposed in aquaria to 100% effluent water and in muscle, liver, kidney, and bile in northern pike (Esox lucius), European perch (Perca fluviatilis) and common rudd (Scardinius erythrophthalmus) from a lake receiving municipal wastewater. Pharmaceuticals were also measured in hepatopancreas of signal crayfish (Pacifastacus leniusculus). In addition to the measurements in fish and crayfish, pharmaceuticals were measured in the effluent, upstream and downstream of the WWTPs. In effluent water, pharmaceuticals were detected in the µg/L range, with the highest concentrations being of commonly prescribed NSAIDs and hypertension drugs, such as diclofenac, ibuprofen, naproxen, losartan, and metoprolol. However, the differences in concentrations between different sampling occasions were high, indicating a need for repeated sampling to obtain representative average concentrations. Pharmaceuticals in fish samples showed strong tendencies to species and tissue-specific partitioning. Levels of diclofenac in the brown trout bile were within the range of 4–16 µg/g w.w and naproxen within 37–170 ng/g w.w, while for all other pharmaceuticals, they were below detection limits. Several other pharmaceuticals were present in a similar order of magnitude in the effluent as diclofenac, suggesting diclofenac has a strong partitioning to trout bile. In the wild fish, the highest number of detected pharmaceuticals and the highest levels were observed in kidney of pike. Diclofenac in pike kidney was at most 37 ng/g w.w, followed by propranolol (20 ng/g w.w) and losartan (18 ng/g w.w). In crayfish, no pharmaceuticals were detected. The results suggest that the kidney of pike is a suitable tissue for evaluating pharmaceuticals in fish, while hepatopancreas of signal crayfish is not.