Clogging is inevitable when membranes with 0.45 µm pore size are used for the separation of particulates from dissolved/colloidal forms in river water. This can lead to a shift in water quality assessment and evaluation of geochemical fluxes. We studied the influence of clogging on the concentration of trace elements, major anions, nitrate, and dissolved organic carbon (DOC) in the filtrates after a sequential pass from 0.1 to 0.5 L of river water samples through the same 47 mm membrane with 0.45 µm pore size. These experiments were carried out for the typical boreal rivers of the Russian Far East, including the biggest one, Amur R., with different quantities of suspended solids (SS) and anthropogenic load. The concentration of the major anions, nitrate, Si, DOC, and such trace elements as Li, B, Ni, Cu, As, Sr, Rb, Mo, Ba, U did not depend on the water volume filtered. However, filterable Al, Fe, Ti, Pb, Mn, Co, and most REEs showed a notable decrease in concentration at an increase in volume filtered, at more than 100–200 mL of river water. Clogging membranes with retention of colloids