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About 70 million rural farm households in Nigeria, out of a population of 180 million lacked access to safe drinking water. In achieving goal six of the Sustainable Development Goals (SDGs) 2030 of ensuring availability and sustainable management of water and sanitation for all, there is need to minimize water-related diseases among the rural farm households using Point of Use (PoU) water treatment systems such as clay and bio-sand filter. The study identifies factors that affect the desirability, acceptability and the amount the rural farm households are willing to pay for clay and bio-sand filters in the study area. The study area was Kaduna and Akwa Ibom states in Nigeria. Multi-stage sampling technique was used for the study. Descriptive statistic, Probit model, Tobit regression model and Choice–based conjoint analysis were used to analyze the data collected. The study revealed that clay filter was the most preferred because of the likeness of the filter design and material with preference index 0.78 and 0.75. The respondents were willing to pay N3, 930 ($10.9) for bio-sand filter. The willingness to pay for clay filter in the study area was influenced by age of respondents, educational level of respondents, estimated monthly income, employment status of respondents, awareness of clay filter, preference level of respondents and price of the clay filter. The study therefore, recommends that bio-sand should be improved upon with respect to its design, size, material, water volume and treatment to make it acceptable like clay filter.