Harmful algal blooms (HABs) are often associated with eutrophication of coastal waters and estuaries. However, identifying quantitative relationships between nutrient input and proliferation of specific algal species is very challenging and complex. The complexity arises from the diversity of sources, forms and fluxes of nutrients both exported into and cycled within the system, the diversity of algal mechanisms for acquiring nutrients, and the interaction of the target harmful species with other members of the food web. Even more challenging is the development of forecasts and predictions, both on the short term and on the long term. Short term scales (days to weeks) are necessary for managers to prepare for, and respond to events; longer scales are needed to enable strategic planning to prevent HAB events, mitigate their impacts, or estimate the interactive effects of anthropogenic activities and climate change. To address these needs the HAB modeling community will need to engage with climate scientists (assess climate change scenarios), marine ecologists (describe organism ecophysiology), invasive species experts, watershed modelers and hydrologists (estimate future changes in the land derived inputs), and socio economists, managers and policy makers (define future land use scenarios and to interpret results in a policy context).