Roman Public Health systems had collapsed as society lacked the money and the technology to maintain them. Public health was therefore generally poor in towns in the Middle Ages:

Towns continued to grow and conditions worsened as little money was spent on improving facilities.
Water quality deteriorated and it was usually contaminated. Drinking water was often taken from the same rivers where sewage was dumped; most people drank beer instead. Cess pits were often built next to wells.
There was no effective sewage system in towns. Where they existed, sewers were often blocked and overflowed. They usually just took sewage to a river or stream. Many toilets were built above rivers.
Streets became even more filthy as towns grew and were full of animal dung, carcasses, human sewage and rubbish.

However there was some progress: Large public baths called stewes were occasionally used by people. Councils tried to enforce laws such as building latrines, banning people throwing remains of animals in the street and fining people for littering. These laws, though, were not very effective.

Monasteries had the best public health facilities as they were built away from towns. They were also wealthy and promoted cleanliness and regular bathing.

People in the countryside were usually healthier as it wasn't overcrowded.

GCSE Health and the People AQA

Public Health in the Middle Ages