Biodiesel from algae may be considered a way of producing biofuels with a carbon footprint less than that of conventional fuels but even here the answer depends on how the algae is grown. If it is grown in open ponds the energy required is less and therefore the CO2 emissions less than conventional diesel. However in open ponds the water required for their growth is subject to evaporation and therefore they can be fairly water intensive. Furthermore they have lower yields than other forms of algae production. High yields can be produced by cultivating algae in closed air lift bioreactors made of transparent tubes but here the amount of energy required to move the algae around to give it enough sunlight makes its carbon footprint considerably greater than that of conventional fossil fuels.
As usual when looking at the issues around climate change and CO2 emission targets the picture is not clear. Looking at the immediate swap of biofuels for fossil fuels would appear to suggest a reduction in CO2 emissions but this is never the whole picture. Biofuels will impact land use, energy input and water; all of which need to be taken into consideration when when building policies around alternatives to fossil fuels.