Lake Malombe is ranked among the most vulnerable inland freshwater shallow lakes in Malawi. The lake has lost over US$79.83 million ecosystem service values from 1999 to 2019 due to rapid population growth, increased poverty, landscape transformation, and over exploitation-hampering the effort to achieve United Nations (UN) Sustainable Development Goals (SDGs), in particular, life underwater (SDG 14), life on land (SDG 15), climate action (SDG 13), and no poverty (SDG 1) and Aichi Biodiversity Targets. In line with the 2021–2030 United Nations' Declaration on massive upscaling of the ecosystems restoration effort, this study applied the contingent valuation method (CVM) and binary logistic regression model to determine the public's willingness to pay (WTP) for ecosystem restoration and the influencing factors. The aim was to integrate science into policy framework to achieve a sustainable flow of ecosystem services (ESs). Qualitative data were collected by employing focus group discussion, key informant interviews, and field observation. Quantitative data were collected using structured questionnaires covering 420 households. The results revealed that 56% of the respondents were willing to pay an average of US$28.42/household/year. These respondents believed that the initiative would improve lake ESs, fish biodiversity, income level, water quality and mitigate climate change impact. Age, gender, literacy, income, social trust, institutional trust, access to extension services, period stay in the area, household distance from the lake, lake ecological dynamics impact, having the hope of reviving the lake health ecological status, perception of having lake ecological restoration program, participation in lake restoration program, access to food from the lake, involved in fishing and Lake Malombe primary livelihood sources significantly (p < 0.05) influenced WTP. This study provides a reference point to policymakers to undertake cost-benefit analysis and develop a practical policy response framework to reverse the situation and achieve United Nations Sustainable Development Goals and Aichi Biodiversity Targets.