In this study, we have chosen a sensitive period, the weaning period, to evaluate in pig farms the effects of different mechanical and chemical waterlines cleaning protocols similar to those used in poultry farms. The experiment has been set up during the down period in two post-weaning rooms with two different protocols. They combined the mechanical action of draining, one detergent (either alkaline or enzymatic), another draining state, and finally one acid used at an antibacterial concentration. To follow the bacteriological quality of water during protocols, we have counted the total flora at 22°C and 37°C in water. Before and after the experiment, cotton swabs were applied into the pipes to evaluate the biofilm. Bacterial concentration in water increased along the pipelines: total flora was higher at watering place than at the entry of the building. Both protocols combining mechanical and chemical procedures reduced total flora, improved water quality and cleanliness of pipes. Our results show that waterlines cleaning protocols used in poultry farms can be transferred in post-weaning rooms. By reducing water’s total flora and the formation of biofilms, they could be part of the health prevention measures for troubles which are linked to a poor water quality.