Yorkshire Water said it was targeting seven locations across the city where there were build-ups of fat deposits.
The firm is deploying organically grown bacillus bacteria, which is commonly found in the human gut, to eat the fat, oils and grease.
The blockages are caused by waste cooking oils from homes being poured down plug holes.
As the fat cools it hardens and deposits gradually build up.
According to Yorkshire Water, in the past six months maintenance crews have attended 1,700 jobs in Hull to remove blockages in local sewers, with 350 jobs carried out in February 2012 alone.
Last year, across its entire 33,500 mile (54,000km) sewer network the firm said it had removed 2,000 tonnes of grease.