The Mulkear catchment has many conservation issues affecting its overall health. The primary issues are:
- Degradation and loss of instream habitat due to river drainage and other land practices. Since the 1850s there have been three major drainage schemes on the river, the latest of which was completed in 1998. In addition, there has been continuous drainage maintenance of the river for flood relief, and this maintenance continues today. The earlier drainage schemes reduced the base level of the river, by up to 4m below the natural river bed levels along the main channel, removed large rock and woody substrate (boulders, logs and other woody debris) and overhanging vegetation. Coarse cobble and gravel was also removed and this substrate is still absent in many parts of the main channel. A consequence of drainage has been the loss of channel length by removal of meander bends, loss in instream habitat by removal of instream substrate resulting in a more uniform channel. The altered channel has also led to significant bank erosion problems which washes silt into the channel potentially impacting on salmon spawning beds. The cumulative effect of these schemes has straightened and simplified the habitat leading to a reduction in fish numbers.
- Several weirs on the Mulkear impede or block the passage of sea lamprey. The weirs are low in the catchment and prevent the lamprey from accessing most of the catchment which they could utilise for spawning and nursery habitat.
- Along sections of the Mulkear River, the riparian vegetation is being overwhelmed by three invasive exotic plants species (Giant Hogweed, Japanese Knotweed and Himalayan Balsam). These plants are known to out-compete native riparian native species (sedges and grasses) which would normally provide food and cover for fish, other aquatic species and other wildlife. Two of these alien species are so strong that they block the light to underlying native grasses in particular. When the alien plants die back in the autumn and winter bare soil is exposed. With no vegetative cover this soil and the associated river bank is subject to erosion causing subsequent siltation on to fish spawning grounds and bank collapse. In addition, Giant Hogweed is hazardous to people. If the sap comes in contact with the skin severe inflammations and blisters will form. The affects can last for a long time and affected areas of skin will be sensitive to sunlight and the skin will easily burn.
- The impact of coniferous forestry plantations within the riparian zone can lead to a reduction in the amount of light reaching the channel and thus reduce the amount of primary production. This in turn can lead to reduced numbers of invertebrates which are the principle food source for juvenile salmonids. In addition, conifer trees provide a less suitable leaf litter which is an important food source for benthic invertebrates.
- Access by cattle to river and streams for drinking and cooling is a problem in the Mulkear Catchment. Cattle access increases faecal fouling of the water which reduces the water quality and consequnetly affects the carrying capacity of the river for fish. In addition, trampling of bank slopes causes erosion and the subsequent siltation of the spawning grounds.
- European otter are known to reside within the Mulkear catchment. However, some stretches of the Mulkear River are lacking in resting areas and holts (homes) for otters. Current drainage schemes remove larger trees and brush along with their associated rooting systems which can provide habitat for otters.