The Regional Monitoring Program (RMP) is transitioning from a watershed program predominantly using monitoring data and data-driven load estimation methods to support management decisions on polychlorinated biphenyls (PCBs) and mercury (Hg) to an integrated modeling and monitoring approach addressing multiple contaminants. In the past, monitoring and modeling approaches used by the RMP were not designed together, leading to greater expense and longer time frames for answering management questions. With increased computational power, enhanced modeling and monitoring experience and capabilities, and rising field program costs, the new integrated modeling and monitoring approach addressing multiple contaminants increases the RMP watershed program’s efficiency. This coupled method can continuously adapt the monitoring program to support modeling that answers the RMP’s near term and long-term watershed management questions, while addressing the broader needs for a watershed-Bay modeling framework that supports estimates of Bay-recovery rates and food web linkage analysis.