The seawater is an abundant source that still not be utilized as potential raw water source to overcome the deficit of drinking water. This paper aims to design the small-scale desalination plant with the capacity of 2000 gpd for treating the brackish and seawater. There are two split processes, i.e., multi-tray aerator and filtration for reducing the Fe and Mn, while the two different type reverse osmosis membranes were used for desalinating process. Parameters used to verify the performance of small-scale plant are salinity and total dissolved solid for membranes, while the parameters for examining the pre-treatment results are TSS, BOD, pH, Fe, and Mn. The test results will be evaluated under the Regulation of The Minister of Health, Number 32/2017. The influence of pump pressure on flow will also be analysed. The results show that multi-tray aerator needs some improvement to reduce the Mn, and Fe. The two types of membranes could significantly reduce the salinity level up to 91.7%, from 22,900 ppm to 1200 ppm. The pump pressure needs to be replaced into the high-pressure pump to reduce the salinity level significantly.