The invention relates to a method and a system for adjusting S/Na-balance of a pulp mill, wherein an aqueous pulp mill liquor containing sulphides is diverted into a bioreactor and oxidized by means of sulphur-oxidizing microbes, thereby producing an aqueous suspension from which elemental sulphur can be separated as a precipitate and the residual solution may be directed to causticizing. Optionally, prior to oxidation in the bioreactor, the aqueous pulp mill liquor may be first stripped to obtain a gas stream containing H2S which is then scrubbed with a scrubbing solution to obtain an aqueous spent scrubbing solution containing sulphides, in which case the residual solution can be used to replenish the scrubbing solution.