Resource allocation is a critical issue for public health decision-makers. Yet little is known about the level and type of resources needed to build capacity to plan and implement comprehensive programs. This paper examines the relationships between investments and changes in organizational capacity and program implementation in the first phase (1998–2003) of the Ontario Heart Health Program (OHHP)—a province-wide, comprehensive public health program that involved 40 community partnerships. The study represents a subset of findings from a provincial evaluation. Investments, organizational capacity of public health units and implementation of heart health activities were measured longitudinally. Investment information was gathered annually from the provincial government, local public health units and community partners using standard reports, and was available from 1998 to 2002. Organizational capacity and program implementation were measured using a written survey, completed by all health units at five measurement times from 1994 to 2002. Combining provincial and local sources, the average total investment by year five was $1.66 per capita. Organizational capacity of public health units and implementation of heart health activities increased both before and during the first 2 years of the OHHP, and then plateaued at a modest level for capacity and a low level for implementation after that. Amount of funding was positively associated with organizational capacity, yet this association was overpowered by the negative influence of turnover of a key staff position. Regression analysis indicated that staff turnover explained 23% of local variability in organizational capacity. Findings reinforce the need for adequate investment and retention of key staff positions in complex partnership programs. Better accounting of public health investments, including monetary and in-kind investments, is needed to inform decisions about the amount and duration of public health investments that will lead to effective program implementation.