Desalination plants have been recently constructed in many parts of the world due to water scarcity caused by population growth, industrialization and climate change. Most seawater desalination plants are designed with a submarine pipeline for intake and discharge. Submarine pipelines are installed directly on the bottom of the water body if the bottom is sandy and flat. Intake is located on a low-energy shoreline with minimal exposure to beach erosion, heavy storms, typhoons, tsunamis, or strong underwater currents. Typically, HDPE (High Density Polyethylene) pipes are used in such a configuration. Submarine pipelines cause many problems when they are not properly designed; HDPE pipelines can be floated or exposed to strong currents and wind or tidal action. This study examines the optimal design method for the trench depth of pipeline, analysis of on-bottom stability and dilution of the concentrate based on the desalination plant conducted at the Pacific coast of Peru, Chilca. As a result of this study, the submarine pipeline should be trenched at least below 1.8 m. The same direction of pipeline with the main wind is a key factor to achieve economic stability. The concentrate should be discharged as much as high position to yield high dilution rate.