The crackdown began after underage sex workers were discovered during a human trafficking raid.
In that operation, officers found evidence that groundwater was being stolen so brothels could avoid paying utility bills - as well as a ledger listing bribes to officials.
Bangkok brothel raid sparks bribery, trafficking probe
Environmental experts say the practice is making Bangkok, already a low-lying city, sink.
Suwat Inthasit, deputy commander of Natural Resources and Environment Crime Suppression Division, said: "Today we will examine the water quality of each room we will go inside."
One of the brothels he suspected of illegally using groundwater was the Embassy Entertain massage parlour, which lies in a notoriously seedy district.
Experts warn parts of Bangkok will be underwater by 2030 because of rising sea levels and groundwater draining into the capital's swampy soil.
The practice of draining groundwater began when the city went through a period of intense development several decades ago.
In recent years, attempts to regulate groundwater usage has dramatically slowed Bangkok's sinking rate.
Thai 'Sin City' finds abstaining from sex hard
At its peak, the capital was sinking at about 10cm a year in the late 1970s.
Prostitution is technically illegal in Thailand, however, it is widely tolerated and openly practiced.
Brothels are common in many parts of Bangkok and no attempts are made to cover up their dealings.
Bribes and loopholes keep the industry afloat, with police largely turning a blind eye.
They do step in if underage women or trafficked sex workers are suspected of working in brothels.
It is not uncommon for officials to be implicated in prostitution scandals, but they rarely face prosecution.