I am sorry to hear that your horse is having diarrhea problems. Diarrhea in horses can be a very serious problem, with a number of various causes. Often times we can have diet changes that "upset" the gastrointestinal system leading to initial loose manure. As this happens, the normal microflora of the intestinal system becomes unbalanced. The organisms that normally present and responsible for normal digestive function are lost faster than they can reproduce. This can allow pathogenic (bacteria capable of causing disease) organisms to then reproduce unchecked, over populating the good bacteria. Common organisms can be Salmonella, Clostridial, E. coli, and other organisms found in the GI system. There are also a large number of viruses that can lead to diarrhea
There are a few things you can try at home to help. I recommend placing your horse on Probiotics to promote a normal population of microflora. The two brands I tend to recommend to my clients are Probios or Propanion. I prefer the top dress granular form to the paste as they are not as environmentally dependent. If the paste is not refrigerated, the bacteria may proliferate and die in the tube rendering them ineffective. Essentially what a probiotic is, a formulation of Lactobacillus acidophilus and Lactobacillus lactis plus a transient bacteria, Bacillus subtilis, which help to normalize digestive function. It is like active yogurt cultures for you and I.
You can also give your horse a Bismuth subsalicylate product like Bismukote (Click here for details). It is essentially Pepto Bismol for horses. You can also use a product called Biosponge to help absorb bacterial toxins. He will also need an electrolyte supplement. If he is still drinking, you can even use the powdered Gatorade products to help provide extra electrolytes.
Providing good quality grass hay is often times easier on their GI system than alfalfa or pasture grass.
The longer diarrhea persists the more likely your horse will become dehydrated and continue to lose essential electrolytes such as Sodium, Potassium, Chloride, and Phosphorus. With dehydration and electrolyte loss, other body systems become affected. Most notably are the cardiovascular and circulatory system.
My recommendation would be to have your veterinarian out to assess your horse, run a CBC and Chemistry screen to assess White blood cell, fibrinogen, lymphocyte counts, electrolyte values, and liver and kidney function. He may also tube your horse with large quantities of the products I recommended earlier. There are times when we will also take a fecal sample to submit for culture and sensitivity to see what pathogenic bacteria are present and if they may be a primary cause of the diarrhea. When Salmonella or Clostridium organisms are causative agents, the prognosis is more guarded.
I hope this information has helped answer your question and can help your horse. If there is anything else I can help you with, please don't hesitate to ask.