The most severe problem is siltation due to soil erosion from the surrounding watersheds. Previous department documents have stated that heavy silt loads, particularly from the East Branch Rock River, contribute to the marsh becoming much shallower in many of its bays and channels. The largest source of sediment to the marsh is soil erosion from agricultural lands. Farming practices such as wetland drainage, fall plowing, farming too close to streambanks, farming on steep slopes and livestock grazing on streambanks all contribute to the marsh's siltation problems. A severe overabundance of carp in the marsh has contributed to decreased water quality.
Carp are able to tolerate poorer water quality conditions than more desirable fish.
The feeding habits of carp muddy the water, uproot vegetation and compete with more valuable fish and wildlife species for invertebrate food organisms. The carp and soil erosion problems are directly linked and the problems with carp will continue as long as the heavy siltation of the marsh continues. The high inflow of nutrients, phosphorus and nitrogen, into Horicon Marsh from surrounding farm fields where manure and other fertilizer is spread, as well as runoff from barnyards and feedlots, is also a serious problem. The nutrients from these sources results in excessive algae and aquatic plant growth which can lead to serious dissolved oxygen problems and may cause fishkills, especially in the winter months. Past water quality monitoring in the marsh has detected levels of pesticides and inorganic fertilizers in the marsh.