This study was conducted to profile the fish farm owners/operators (known as fish farmers) at the Marilao-Meycauayan-Obando River System (MMORS) and to determine their current fish farm management practices (FFMPs) and concerns encountered in fish farming. Characterizing the fish farmers enabled the formulation of appropriate adaptation interventions that may serve as inputs for management strategies and rehabilitation efforts to address water pollution. In doing so, sustainable fish production could be assured. Focus group discussions, key informant interviews, and a survey were conducted. The survey sampling size was proportionally allocated among municipalities covered in this study. Half of the respondents were full-time fish farmers and received an estimated monthly income of USD 125–250. The majority (60%) managed small ponds (4 ha and below), which were used for rearing and nursery or rearing and transition of fingerlings or fry. Many rented fish farms through lease agreement with private owners (78%); they mostly grew milkfish (74%) and tilapia (41%), but a few also raised prawns (18%) and shrimps (12%). The fish farmers’ major issues include flooding due to changing climate patterns (74), water pollution (21), and presence of invasive species (20). Their adaptation strategies include technological changes including FFMPs. However, institutional arrangements are crucial to ensure sustainability and productivity. The study recommends the adoption of an integrated social-technological approach called CARE solution, which refer to Community Action by organizing the fishery sector; long-term Rehabilitation by integrating efforts of all stakeholders through the MMO Water Quality Management Area Board; and Enforcement of environmental laws. This approach is congruent with the Ecosystem Approach for Aquaculture that integrates ecosystem, human well-being and equity, and incorporates other sectors for aquaculture development and management. The fish farm management baseline study results could be an input in developing specific interventions using the CARE solution framework in the MMORS cleanup and rehabilitation. This approach could help in the design of interventions that aim to achieve enhanced socio-ecological health and ecosystem services for improved and sustained socioeconomic productivity.