Macroalgae harvested along coastlines and in the open ocean has traditionally been used as food for human consumption, animal feed, and fertilizer. The U.S. ARPA-E MARINER Program estimates that the nation has suitable conditions and geography to produce at least 500 million dry metric tons of macroalgae per year, yielding approximately 2.7 quadrillion BTUs of energy in the form of liquid fuel, which is roughly 10% of the nation’s annual transportation energy demand. Adverse environmental effects of nutrient overload and ocean acidification may also be reduced by large-scale macroalgae cultivation in many coastal ocean regions. However, the successful deployment of large-scale marine macroalgae farms for fuel production depends on ambient hydrodynamic conditions and nutrient availability, as well as their interactions with macroalgae farm structures. Pacific Northwest National Laboratory led an ARPA-E MARINER project to develop a set of numerical modeling tools capable of simulating ocean hydrodynamic and biogeochemical processes, macroalgae trajectories for free-floating systems, macroalgae growth and biomass yields, and hydrodynamic load on macroalgae canopies and farm structures using a multi-resolution and multi-scale approach. This set of modeling tools provides a suite of information essential for system design, optimal project siting, risk analysis, and management of macroalgae production systems in the ocean. Better clarity can also help macroalgae system developers reduce deployment costs, operational risk, and potential impacts on the local marine environment.