While alien vegetation is the primary ecological threat in the reserve, there are other matters that are of significant concern.
Modderfontein Reserve is located in an urban area and so is subject to a fair amount of water pollution from surrounding human activities.
The water quality is thus not of a very high standard. Litter brought down from upstream contributes to the polluted nature of the water bodies and this affects all water dependent organisms.
Soil erosion causes a loss of topsoil and an increase in runoff rainwater. This creates a hostile environment for the growth of vegetation, particularly less aggressive indigenous plants, and measures must be taken to improve veld condition through erosion control measures.
Due to the sandy soils and the sloping topography in many parts of the reserve, erosion is a significant problem and erosion work is under way in certain sections in an attempt to remedy the effects of the loss of topsoil. Two sites in particular have been addressed through the construction of erosion dams with the help of scouts and Nature Conservation students.