It depends how far in the past you're looking. Post-agriculture but pre modern sanitation, yes diarrhoea is a major problem. Pre-agriculture, however would have been a different matter. The majority of pathogens in river water are derived either from agriculture (e.g. cryptosporidium, giardia) from large human populations (cholera) or rodents associated with human populations (leptospira). There would, therefore have been far fewer disease causing organisms in river water Pre-agriculture. Add to that the effect on the immune system of Post-agriculture diet and lifestyle and it would seem unlikely that the cleanliness of most river water would have been a major problem.