Pressurized powdered activated carbon/coagulation/ceramic microfiltration (PAC/Alum/MF) was investigated at pilot scale for treating low turbidity and low natural organic matter (NOM) surface waters spiked with organic microcontaminants. A total of 11 trials with clarified or non-clarified waters spiked with pesticides, pharmaceutical compounds, or microcystins were conducted to assess the removal of microcontaminants, NOM (as 254 nm absorbance, A254, and dissolved organic carbon, DOC), trihalomethane formation potential (THMFP), aerobic endospores as protozoan (oo)cysts indicators, bacteriophages as viruses indicators, and regular drinking water quality parameters. PAC/(Alum)/MF achieved 75% to complete removal of total microcontaminants with 4–18 mg/L of a mesoporous PAC and 2 h contact time, with a reliable particle separation (turbidity < 0.03 NTU) and low aluminium residuals. Microcontaminants showed different amenabilities to PAC adsorption, depending on their charge, hydrophobicity (Log Kow), polar surface area and aromatic rings count. Compounds less amenable to adsorption showed higher vulnerability to NOM competition (higher A254 waters), greatly benefiting from DOC-normalized PAC dose increase. PAC/Alum/MF also attained 29–47% NOM median removal, decreasing THMFP by 26%. PAC complemented NOM removal by coagulation (+15–19%), though with no substantial improvement towards THMFP and membrane fouling. Furthermore, PAC/Alum/MF was a full barrier against aerobic endospores, and PAC dosing was crucial for ≥1.1-log reduction in bacteriophages.