Pharmaceuticals (a class of emerging contaminants) are continuously introduced into effluent-receiving surface waters due to their incomplete removal within wastewater treatment plants (WWTPs). This work investigated the presence and distribution of eight commonly used human pharmaceuticals in the River Dee (Scotland, UK), a Scottish Environment Protection Agency priority catchment that is a conservation site and important raw water source. Grab sampling and passive sampling (Polar Organic Chemical Integrative Sampler, POCIS) was performed over 12 months, targeting: paracetamol, ibuprofen, and diclofenac (analgesics/anti-inflammatories); clarithromycin and trimethoprim (antibiotics); carbamazepine and fluoxetine (psychoactive drugs); and 17α-ethynylestradiol (estrogen hormone). Sampling sites spanned from the river’s rural source to the heavily urbanised estuary into the North Sea. Ibuprofen (ranging 0.8–697 ng/L), paracetamol (ranging 4–658 ng/L), trimethoprim (ranging 3–505 ng/L), diclofenac (ranging 2–324 ng/L) and carbamazepine (ranging 1–222 ng/L) were consistently detected at the highest concentrations through grab sampling, with concentrations generally increasing down river with increasing urbanisation. However, POCIS revealed trace contamination of most compounds throughout the river (commonly <0.5 ng/L), indicating pollution may be related to diffuse sources. Analysis of river flows revealed that low flow and warm seasons corresponded to statistically significantly higher concentrations of diclofenac and carbamazepine, two compounds of environmental and regulatory concern. Below the largest WWTP, annual average fluxes ranged 0.1 kg/yr (clarithromycin) to 143.8 kg/yr (paracetamol), with 226.2 kg/yr for total target compounds. It was estimated that this source contributed >70% of the total mass loads (dissolved phase) of the target compounds in the river. As the River Dee is an important raw water source and conservation site, additional catchment monitoring is warranted to safeguard water quality and assess environmental risk of emerging contaminants, particularly in relation to unusual weather patterns, climate change and population growth.