There is a growing concern that long-standing, expanding environmental changes in resource degradation accompanied by rapid economic growth are affecting the health and livelihoods of people in many parts of Asian countries. These vulnerable communities live in degraded ecosystems that are harmful to their health. With few resources to face these problems, they face environmental pollution, and new and old infectious diseases. The present paper is an outcome of an ongoing empirical research, composed of medical, environmental and social scientists, to clarify the link between environment degradation, leading to a disruption of ecosystem services, and people’s health and livelihoods. More specifically, it is our aim to identify and analyze the past and current land use changes, water and sediment related risks to the health of communities in the Laguna Lake region in the Philippines and the linkage with their livelihoods. It is expected to clarify more practical, appropriate policy recommendations to improve current land use and development planning as well as public health systems. For data collection, household surveys, focused group discussions, key informant interviews are conducted in addition to secondary data reviews. Laboratory analyses are conducted with soil, water, biomaterial and fish samples to identify ecological risks at upper, middle and lower watersheds. Data analysis is conducted by using statistical and geographical information system tools. The challenge of the ecosystem approach to Eco-Food system is how to meet human needs without modifying or jeopardizing the ecosystem in the long term, and ideally, even improving it.