Objectives: The Affordable Care Act created new resources and incentives for hospitals, insurers, public health agencies, and others to contribute to disease prevention and health promotion activities, potentially changing the structure of public health delivery systems and expanding the implementation of strategies that improve population health. This study uses data from the 1998-2014 National Longitudinal Survey of Public Health Systems to examine: (1) the extent and nature of change in inter-organizational contributions to public health activities, which we use as indicators of public health system change; and (2) the effects of these changes on preventable mortality and resource use. Methods: Our retrospective cohort design follows 354 U.S. metropolitan communities over time using survey data collected initially in 1998 and again in 2006, 2012 and 2014. Local public health officials report on the availability of 20 recommended public health activities in the community, the organizations that contribute to each activity, and the perceived effectiveness of each activity. We classify communities into one of seven categories of “system capital” based on a cluster analysis of the scope of activities contributed by each type of organization, along with network-analytic measures of inter-organizational connectedness in performing activities (density, degree and betweenness centrality). We link survey data with outcome measures that include county-level cause-specific mortality rates and measures of public health agency expenditures from secondary data sources. Fixed-effects models with instrumental-variables are used to estimate changes in preventable mortality and expenditures attributable to changes in system capital, while controlling for observable and unmeasured confounders. Results: Communities with the highest levels of system capital based on scope of activity and inter-organizational connectedness increased from 24% of the sample in 1998 to 37% in 2006, but fell to 31% in 2014. In total, 36% of communities gained system capital over 1998-2014 as indicated by their cluster category, while 45% lost system capital. Increases in system capital were associated with statistically-significant reductions in infant mortality and deaths due to cardiovascular disease, diabetes, and cancer. System capital had nonlinear effects on public health resource use, with expenditures declining at the highest levels of system capital. Conclusions: Comprehensive and highly-integrated public health systems appear to offer considerable health and economic benefits over time. Opportunities exist for improving population health through policy initiatives to build public health system capital, such as through the ACA’s hospital community benefit provisions and the IOM’s call for a minimum package of public health services.