To permit the use of bio-diesel without mixing and without the possibility of gelling at low temperatures, some people modify their vehicles with a second fuel tank for bio-diesel in addition to the standard fuel tank. Alternately, a vehicle with two tanks is chosen. The second fuel tank is insulated and a heating coil using engine coolant is run through the tank. When a temperature sensor indicates that the fuel is warm enough to burn, the driver switches from the petrodiesel tank to the bio-diesel tank

Contamination by water :

Bio-diesel may contain small but problematic quantities of water. Although it is hydrophobic (non-miscible with water molecules), it is said to be, at the same time, hygroscopic to the point of attracting water molecules from atmospheric moisture, one of the reasons bio-diesel can absorb water is the persistence of mono and diglycerides left over from an incomplete reaction. These molecules can act as an emulsifier, allowing water to mix with the bio-diesel. In addition, there may be water that is residual to processing or resulting from storage tank condensation.

The presence of water is a problem because:

1-Water reduces the heat of combustion of the bulk fuel. This means more smoke, harder starting, less power.
2- Water causes corrosion of vital fuel system components: fuel pumps, injector pumps, fuel lines, etc.
3-Water & microbes cause the paper element filters in the system to fail (rot), which in turn results in premature failure of the fuel pump due to ingestion of large particles.
4-Water accelerates the growth of microbe colonies, which can plug up a fuel system. Bio-diesel users who have heated fuel tanks therefore face a year-round microbe problem.
5-Additionally, water can cause pitting in the pistons on a diesel engine.

Energy security

One of the main drivers for adoption of bio-diesel is energy security. This means that a nation's dependence on oil is reduced, and substituted with use of locally available sources, such as coal, gas, or renewable sources. Thus a country can benefit from adoption of biofuels, without a reduction in greenhouse gas emissions. Whilst the total energy balance is debated, it is clear that the dependence on oil is reduced.