Articles and scientific papers about desalination. There lots of issues but power consumption and toxic discharge are the main culprits.

First off, here is what MIT has to say about Desalination:
Brine Disposal
Brine, or the high-salinity concentrate that is removed from water during desalination, has traditionally been deposited in landfills or oceans, but this is not an environmentally viable plan for the next 100 years. The TDS, or total dissolved solids, concentration for brine is at least 36 kg/meters cubed.(Younos, 2, 2005) Simply dumping the brine into the ocean, as is tradition for some facilities, will wreak havoc for organisms living in the water that may be accustomed to the homogenous conditions of the water. Not only does brine have environmental impacts, but also efficiency issues. For every 100 gallons that enters a desalination plant, only 15-50 gallons exit as freshwater, (Cooley, Gleick, & Wolff, 2008) while the remainder consists of brine. If we defined desalination efficiency as the percentage of products used, we hope to use brine so desalination's efficiency increases to over 75%. In fact, brine may play an important role in our aforementioned solutions.
As discussed earlier, co-location with power plants eliminates the need and cost for new intake pipelines. In this scenario, brine is typically discharged into a cooling water pipeline, which pumps the dilute solution into an injection well. Leaks from these wells bring a risk to the water quality of nearby underground aquifer, and so land application of brine is a safer approach. A common tool for brine disposal is an evaporation pond. Evaporation ponds work well in arid areas, such as the west coast of America, because they collect concentrate in a basin as water in the brine evaporates. There are currently no evaporation ponds in California used for brine disposal, and we believe this solution will eliminate the need for further discharge lines and facilities and provide salt processing factories with a harvest of sodium chloride. The salt could then be used for industrial processes such as the manufacture of glass, the production of detergents, polymer production, tanning, aerospace alloys, effluent neutralisation, metal refining, sugar extraction and cement manufacture. (University College Worcester, 2000) For these reasons, we would like to add double-lined evaporation ponds to open areas where populations would not be disturbed. Specifically, we are looking at the desalination plant in Morro Bay and the Hearst San Simeon State Historical Monument plant because the population is approximately 50-99 people per square mile compared to Los Angeles County, where the population reaches tens of thousands of people per square mile. Additionally, these two plants are located nearby two power plants. Co-location coupled with the use of evaporation ponds in California decreases desalination's impact on the ocean and increases the efficiency of desalination.
Environmental Issues
Critics of desalination are quick to point out that this process may pose threats to the environment, but our solutions were chosen specifically to help combat the environmental issues resulting from desalination. When brine is excessively emptied into the ocean, sensitive organisms such as sea urchins and precious habitats such as coral reefs can be harmed. We recognize that in areas where there is no space for an evaporation pond or seawater disposal is more feasible, brine disposal has the lowest effect on nature in areas of rocky, sandy shores since brine will sink down rather than mix and coast-parallel currents to sweep the brine away. Additionally, we will strive to avoid disposing of brine in area near salt marshes, coral reefs, and mangrove flats. This means that any desalination plant near San Francisco Bay, such as the proposed Marina Municipal Water District desalination plant, should use evaporation ponds to cut down on the amount of brine being put into to ocean and further co-location with the Portrero Unit 3 thermal power plant to water down the brine that actually does enter the ocean. In fact, this concern is one reason why the Monterey Bay Desalination Plant is co-located with the Aquarium, which happens to be the largest of its kind in the US. To further avoid contamination, we also would like to see the construction of a new salt processing plant that would put the brine to industrial uses. Ideally, this new plant would be located south of Moss Landing and Monterey Bay, where it would not disturb a large population and where there is a need for continued environmental stability.
Desalination has been found to add up to 25kg of carbon dioxide to the atmosphere per meter cubed of water produced. (Water Week, 2007) In a time of increased awareness of global warming, we know that our solution has to combat greenhouse gas emissions. We also strive to disturb communities as little as possible. Our use of wind energy will both help the environment and the community because it has been proven to decrease carbon dioxide emission while operating quietly. According to our calculations, 1500 kWh of energy will be produced per year for every 1 kW per turbine. Wind can provide energy at a rate as low as $.05/kWh. (American Wind Energy Association, 2008) To put this in perspective, the Chevron Desalination Plant in California, a proposed site for wind turbines, requires 6.9 million kWh/yr. This particular reverse osmosis facility has a capacity of 460 AF per year and the operation costs come to $4000/AF. (Frum, 2008) Using these numbers, the total cost for desalination at this plant would be $1.8 million/yr. If all of the energy required to run the facility was provided by the wind, the energy costs would only come to $345,000. These savings, as well as those from using wind energy at the Ventura and Metro Water District of Southern California desalination plants, will stop millions of pounds of gases from being released into the atmosphere.
Solar energy, much like wind energy, will cut down on greenhouse gas emissions. The Santa Barbara desalination plant, which, as we mentioned at the beginning of our solution statement, has been decommissioned, is estimated to require 49.5 million kWh/yr (Frum, 2008) and would release 35,000 metric tons of carbon dioxide into the atmosphere annually. This is an extreme case, but it shows just how careful we have to be when proposing desalination as a solution. Our use of solar ponds and solar stills acts as a supplement to desalination, not an alternative.