Invasive species affect the structure and processes of ecosystems they invade. Invasive species have been particularly relevant to the Laurentian Great Lakes, where they have played a part in both historical and recent changes to Great Lakes food webs and the fisheries supported therein. There is increased interest in understanding the effects of ecosystem changes on fisheries within the Great Lakes, and ecosystem models provide an essential tool from which this understanding can take place. A commonly used model for exploring fisheries management questions within an ecosystem context is the Ecopath with Ecosim (EwE) modeling software. Incorporating invasive species into EwE models is a challenging process, and descriptions and comparisons of methods for modeling species invasions are lacking. We compared four methods for incorporating invasive species into EwE models for both Lake Huron and Lake Michigan based on the ability of each to reproduce patterns in observed data time series. The methods differed in whether invasive species biomass was forced in the model, the initial level of invasive species biomass at the beginning of time dynamic simulations, and the approach to cause invasive species biomass to increase at the time of invasion. The overall process of species invasion could be reproduced by all methods, but fits to observed time series varied among the methods and models considered. We recommend forcing invasive species biomass when model objectives are to understand ecosystem impacts in the past and when time series of invasive species biomass are available. Among methods where invasive species time series were not forced, mediating the strength of predator–prey interactions performed best for the Lake Huron model, but worse for the Lake Michigan model. Starting invasive species biomass at high values and then artificially removing biomass until the time of invasion performed well for both models, but was more complex than starting invasive species biomass at low values. In general, for understanding the effect of invasive species on future fisheries management actions, we recommend initiating invasive species biomass at low levels based on the greater simplicity and realism of the method compared to others.