Horizontal and slant wells are being investigated as a means of obtaining feed water for seawater reverse osmosis (SWRO) desalination plants. These well types have been touted to produce higher quality seawater that will reduce the rate of membrane biofouling by removing algae, bacteria, transparent exopolymer particles, and other fractions of natural organic matter similar to onshore wells located on the beach. As these new well types are being considered for large-scale use, a careful evaluation of the biogeochemistry of seawater that occurs within the near shore subsurface sediments is necessary to assess potential impacts to the SWRO process train. A high percentage of the coastlines of the world contain offshore sediments with seawater that is anoxic in nature with significant concentrations of hydrogen sulfide and dissolved organic matter, iron, manganese, and heavy metals. Where dissolved iron and/or manganese occur at concentrations greater than 1 mg/L in raw seawater, the raw water quality can be problematical for direct treatment using the SWRO process. Membrane scaling and biofouling could become issues, which may necessitate pretreatment to reduce dissolved iron and manganese to acceptable concentrations prior to entry into the membrane process. The anoxic nature of the water could complicate the pretreatment process to remove the dissolved metals. Pretreatment requirements could significantly raise the capital and operational costs of SWRO negating the economic advantages of subsurface intakes. Six SWRO cost scenarios were evaluated to assess the impacts of slant wells on capital and operating costs based on the necessary to remove or not remove dissolved iron and manganese. The capital cost comparison of two open-ocean intake pretreatment to systems using slant wells shows an increase of 4.5 to 13%. The difference in operating costs can range from 19% lower to 56% higher depending on the pretreatment required.