In the present work, the analysis of seven fullerenes (C60 and C70 fullerenes and five functionalised fullerenes) has been performed in river samples collected in the vicinities of Barcelona (Catalonia, NE of Spain). The results of 48 samples (25 river waters, 12 river sediments and 11 wastewater effluents) are presented. Extracts of river water, river sediments and wastewater effluents were analysed by liquid chromatography (LC), using a pyrenylpropyl group bonded silica based column, coupled to a high-resolution mass spectrometer (HRMS), using a dual ion source, atmospheric pressure photoionisation/atmospheric pressure chemical ionisation source (APPI/APCI). The novel methodology presents good chromatographic separation, excellent selectivity and instrumental limits of quantification (ILOQ) in the femtogram order. Method limits of quantification (MLOQ) ranged from 2.9 to 17 pg/l and from 3.2 to 31 pg/l in surface waters and wastewaters, respectively. In wastewater effluents, the sums of C60 and C70 ranged from 0.5 to 9.3 ng/l. In surface waters, C60 fullerene was the most ubiquitous compound, being detected in 100% of the samples in concentrations from 31 pg/l to 4.5 ng/l, while C70 concentrations ranged from less than the method limits of detection (MLOD) to 1.5 ng/l. The presence of fullerenes in both the large particulate (diameter Ø > 450 nm) and the colloidal (Ø < 450 nm) fractions of surface waters should be noticed. In sediments, the concentrations of fullerenes were between the MLOD and 34.4 pg/g. In addition, nanoparticle tracking analysis (NTA) was used for the characterisation of water samples in terms of nanoparticle number concentration and size distribution. As far as our knowledge is concerned, this is the first time that NTA has been used for the characterisation of complex river waters with an environmental focus.