Free Faecal Water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. The cause of FFW is unknown, and it was hypothesized to involve the gut microbiota. This hypothesis was addressed as follows. Firstly, comparison of the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n=10). Secondly, treatment of FFW horses with a standardised Faecal Microbiota Transplantation (FMT) protocol (n=10) followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (P >0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (P = 0.02) and remained decreased for the remainder of the study (P <0.02). However, individual animal responses to FMT varied. In terms of FMT effects on faecal prokaryotic community composition, only alpha diversity was affected with a temporary decrease directly following FMT (P <0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, FMT can temporarily alleviate FFW symptom severity without causing changes in the faecal microbiota.