The invention concerns a method for controlling a nanofiltration or reverse osmosis module system designed for treating a supply fluid or for detecting living micro-organism leaks, each module comprising nanofiltration or reverse osmosis membranes and joints connecting said membranes, including steps which consist in: selecting in the supply fluid a dissolved compound present in significant amount but normally highly retained by the membranes; measuring the concentration value of said compound in a downstream zone of a module of said system; comparing said measured value with a reference value; and recognising the existence of a fault in said zone of the system when said measured value is higher than the reference value.