One of the many points upon which California High Speed Rail has tried to sell itself is in the fact that it will be a carbon free form of transportation, responsible for no CO2 emissions in its normal operations, unlike air and automobile travel, both of which are dependent upon greenhouse gas releasing fossil fuels. While California's electricity is significantly less polluting than the national average, it still isn't entirely free of pollutants, releasing 0.819 pounds of CO2 equivalent per kilowatt hour (2009, calculated from page 3; note that imported electricity is significantly dirtier than that produced in California itself and the amount of imports per year can cause significant changes in electrical CO2 emissions).
In order to get rid of this small amount of greenhouse gas generation, the Authority plans on spending a premium of 3.09 cents per kilowatt hour for "green power." This comes to a fairly staggering premium of $83.20 per metric ton of CO2. This premium is even higher if compared to simply buying domestically generated electricity which, at 0.661 pounds per kilowatt hour, comes out to $103.10 per metric ton of carbon dioxide. By the time that high speed trains actually begin running, the carbon intensity of California electricity will be even lower and the resulting premium for "green power" consequently higher.
Now, this may very well be a more accurate price for carbon than conventional estimates or California's cap and trade auction price of $10 per metric ton, but it seems quite odd to spend substantial sums of money simply for the sake of bragging rights. Indeed, even the Authority does not go so far in its benefits analysis, attributing a social cost of carbon that reaches only $48.71 (in 2011 dollars) by 2050 (page 21).
As far as paying this premium as an advertising strategy goes, this is a rather pricey means for dubious gains. Those who choose their method of travel at least partially based upon carbon emissions are not likely to be dissuaded from a trip because it contributes 19 pounds of CO2e and could, in any event, be easily induced to pay a token amount of money for a carbon offset. However, the appeal of high speed rail, for nearly all potential travelers, is going to be from other factors than the amount of carbon generated.
Now, is the total amount of money spent on this a terribly large sum? To a certain degree, yes. The Authority's medium scenario estimates are for 8.9 million, 16.3 million, and 21.1 million train-miles annually for the initial operating system, Bay to Basin, and Phase 1 Blended plans (page 12) as well as 59 kWh per train-mile (ibid, page 7). This translates to annual costs of $16.2 million, $29.7 million, and $38.5 million (2011$) in order to run the high speed rail system without carbon emissions. Looking at the year 2040 that the mileages are evidently for, the carbon free premium for the Phase 1 Blended represents just over 4% of total O&M costs. It's not too terribly large a portion of the total budget, but I find it a waste of taxpayer dollars to spend that much money on self-congratulatory "green power" instead of purchasing significantly cheaper offsets.