Low-cost household water treatment systems are innovations designed to improve the quality of drinking water at the point of use. This study investigates how an NGO can design appropriate programme strategies in order to increase the adoption and sustained use of household sand filters in rural India. A system dynamics computer model was developed and used to assess 18 potential programme strategies for their effectiveness in increasing filter use at two and ten years into the future, under seven scenarios of how the external context may plausibly evolve. The results showed that the optimal choice of strategy is influenced by the macroeconomic situation, donor funding, presence of alternative options, and the evaluation time frame. The analysis also revealed some key programme management challenges, including the trade-off between optimising short- or long-term gains, and counter-intuitive results, such as higher subsidy fund allocation leading to fewer filter distribution, and technology advances leading to fewer sales. This study outlines how an NGO can choose effective strategies in consideration of complex system interactions. This study demonstrated that small NGOs can dramatically increase their programme outcomes without necessarily increasing operational budget.