Introduction Fishes and shellfish not only contribute to food and nutrition security but also to the livelihood of coastal communities in the Philippines. However, some fishing grounds are contaminated and health advisories against seafood consumption are issued, which may negatively affect the fishing communities’ livelihood. This study aimed to assess fish and shellfish consumption of households living in selected coastal barangays of the Marilao-Meycauayan-Obando River System ( MMORS). The food systems framework was applied whereby fish and shellfish consumption and livelihoods were viewed as part of a larger food system. Methods: The study was conducted in five barangays of the MMORS. A total of 110 household respondents were selected based on systematic random sampling. Key informants were interviewed to determine fish farm production and distribution. The final questionnaire included questions on socio-demographic information, household consumption information on frequency of consumption of fishes and shellfishes, sources of produce, fish and shellfish preparation and cooking methods, and perceptions on the fish produce in the area. Data were encoded and tabulated while qualitative data were analysed using thematic analysis. Results: Fishes and shellfishes are grown in earth-diked fish ponds using river water or harvested along the river system. No post-harvest processing is done and harvests are directly sold in fish markets within the area or nearby towns depending on the price and size of harvests. Fish consumption in both areas is affected by taste, tradition, price, nutritional value, age, gender and intra-household roles, and is found to be higher compared to national levels in the Philippines. Conclusion: The feedback of health and nutrition advisories which are based on food consumption patterns to other food outcomes like livelihoods and ecological health were included in this study. Based on the findings, it is suggested that appropriate interventions should be implemented to balance food system outcomes.