There is ample research available regarding the benefits of soaking hay: 1) to reduce water soluble carbohydrate content for horses that may be sensitive to sugars, such as those with insulin resistance, equine metabolic syndrome or polysaccharide storage myopathy; and 2) to reduce molds and particles that might be problematic for horses with heaves or other respiratory issues.

However, the addition of water to forage may, in fact, activate dormant microbial spores or pathogens. Müller, Nostrell and Bröjer conducted a study to determine the effect of storage time and water soaking on microbial counts in different types of forages, and this was published in the Journal of Equine Veterinary Science in July 2015.

These authors produced silage (harvested at 40% dry matter), haylage (harvested at 60% dry matter) and hay (baled at 80% dry matter) that was then stored for three months or 12 months. Once opened, the silage, haylage or hay was sampled and then soaked with water at 5-7°C for 24 hours.
Results found that mold was higher in hay than silage or haylage after storage of three or 12 months, but these values in hay decreased after soaking (though were still higher than haylage or silage). Prolonged storage (12 months) decreased mold counts in hay, but these were still higher than silage or haylage. Soaking tended to increase yeast counts, and increased enterobacteria counts, which were already high in the hay samples. Silage had higher amounts of lactic acid bacteria, followed by haylage and then hay had the lowest amounts, however, the amounts in the haylage were not considered problematic.

These findings suggest that soaking hay may have some negative consequences, and owners should discuss the best soaking method and/or forage source for their horses depending on the horse’s requirements.