Actually, malaria is spread by insect vector - namely, mosquitoes. Aside from that, Tom's pretty spot on about how virulent waterborne infections can be; with cholera and norovirus being the classic examples. Speaking of insect vectors, that could be an alternative solution to spreading the disease. Namely, the insects breed at a particular water source before they mature and spread the disease.
Back on the subject of waterborne infections, it might be worth a ponder figuring how you want your disease to work. How does Tibetan Muscle Deterioration cause muscle deterioration? Are the muscles breaking down? Why? How?
As can be seen by my examples, waterborne infections have a tendency to cause gastrointestinal problems - diarrhoea and vomiting (D&V) - which isn't all that surprising, since that's where the pathogens are introduced and frequently sit in the host's body. However, there are some viruses such as Hepatitis A that do regularly cause non-D&V related symptoms.
Something to consider is that some pathogens cause symptoms not by their presence alone but through the production of toxins (chemicals) that react with host cells, causing the latter to produce an inappropriate response.
In addition, there's a condition/symptom called "rhabdomyolysis" which is the rapid breakdown of (normally damaged) skeletal muscle. It has a variety of causes, some of which do include bacteria and viruses. Just food for thought, really.
Hope this helps and happy writing.