High DOC suggests wetlands to me.  Wetlands can reduce ionic mercury to methyl mercury and that may bioaccumulate.  Predatory fish seem to be the ones that are most affected, but also they have found MeHg accumulaion in mosquito fish.  High DOC also has some public water treatment issues with bromide in chlorination.  Too much DOC may affect productivity.  I am unsure if there are levels of concern or if there may be other effects, so hopefully you will get other advice.  To reduce the sulfate reduction of mercury, I have thought the addition of lime may alter or reduce the reduction.  Acid waters also suggest possible Aluminum concerns, but I am unsure if the acidity related to dissolved carbon is the same effect.  If culturing as food, perhaps a few tests may satisfy your concerns.

It very much depends on the fish species you wish to culture. Some estuarine fish such as Galaxiids require a very  high organic carbon content in the water to thrive, Oceanic fish such as Mahi Mahi will not thrive at all, they require very clear clean water. Rift Valley lake fish from Africa also have specific trace mineral requirements, Axolotyls prefer a high Magnesium content.

Having said all that, you can reduce the organic carbon in the water by using charcoal filters and aeration, Activated charcoal is best, but ordinary charcoal will do.  Its more cost effective to combine the filtration with partial recirculation of the filtered water.

Various guidelines for maximum rates of input of organic matter have been estimated on theoretical grounds taking into account factors such as rates of dispersion, resuspension and microbial decomposition . some researcher estimated theoretical maximum rates of assimilation of organic carbon by sediments based on the ability of local water currents to supply enough oxygen to prevent the overlying water from becoming anoxic. They used this model to predict situations where sediments would become anoxic and mats of anaerobic bacteria would develop. Empirical data have also been used to develop guidelines, such as correlations between rates of input and loss of diversity of the benthic fauna.