Walleye (Sander vitreus) are currently managed by regulations, stocking, and habitat manipulation, much of which is predicated on our understanding population size and recruitment status (i.e., recruitment classification). Our understanding of the linkages between walleye recruitment status with actual recruitment rates, habitat availability, and genetic diversity and structure is unclear. A fundamental challenge in our management of walleye is the incorporation of relevant scientific data from the vast number and diversity of walleye population types into a comprehensive management approach. Despite strong efforts, our understanding of interactions between population recruitment dynamics, habitat availability, and genetic characteristics of walleye populations are largely unknown. It is reasonable to expect the short- and long-term viability of walleye populations to be directly linked to this series of complex interactions. Thus, evaluating the population recruitment patterns, habitat availability, and genetic diversity can provide a template for a wide array of management decisions. The overarching goal of this research project is to evaluate the role(s) population dynamics, genetics, and habitat has on the recruitment status and viability of Wisconsin’s walleye populations. The specific objective of this current phase of the project is to determine if a relationship(s) exist between walleye habitat availability and quality, recruitment status, genetic diversity, and the effective number of breeders in a sample of Wisconsin walleye lakes. The first phase of this research is testing if commercially available side-scan and down-scan sonar units can effectively enumerate littoral zone habitat in north temperate lakes compared to a traditional, random transect visual method. The second phase of this research is to determine univariate and multivariate relationships comparing data describing spawning and littoral zone habitat, population dynamics, age and growth, and genetic diversity.