The main problem with fresh water is that it is not the medium in which most divers were trained. Thus, their buoyancy appreciation is distorted. Acceptable weights in sea water may be excessive in fresh water. Depth gauges are calibrated for sea water, and so they need to be corrected for diving in dams, lakes, quarries and so forth. Because these waters are often stationary, there may be dramatic thermoclines, requiring adjustments for thermal protection and buoyancy, as one descends.
There are also many organisms that are destroyed by sea water but that thrive in warm fresh water. Some of these, such as Naegleria, are fatal.