Increased understanding of the causes and consequences of recruitment variability is needed to develop effective strategies for sustaining fish populations and fisheries. Recruitment, a fundamental biological process governing the status and trajectory of populations, is regulated by a suite of biophysical processes acting on the growth and survival of early life-stages. In the Laurentian Great Lakes, disentangling the drivers of declining, poor, and sporadic recruitment is a key knowledge gap for sustaining Lake Whitefish (Coregonus clupeaformis) and Cisco (C. artedi) populations and fisheries. This dissertation examined the early life-history and recruitment variability of these two ecologically, culturally, and economically significant species. I characterized and compared species-specific dynamics across the Great Lakes, which span multiple gradients of biophysical ecosystem structure and anthropogenic disturbance. I began by investigating larval spatial ecology across physical habitat gradients and through ontogeny. Results affirmed that Cisco and Lake Whitefish larval life-histories are highly similar and did not support the hypothesis that larval habitat use differences are a major driver of divergent recruitment. Next, I synthesized current understanding of the important drivers of recruitment variability and mechanisms by which they act to regulate recruitment among lakes. This study achieved a holistic review of recruitment drivers across lakes and species by bridging knowledge derived from individual studies of a single driver, species, and/or lake. I went on to reconstruct long-term recruitment dynamics of these two species across the Great Lakes and Lake Simcoe. Results demonstrate that these species exhibit fundamentally different dynamics in recruitment to the adult population, despite sharing similar early life histories. Lastly, I built upon these results by quantifying the suite of important biophysical drivers of Lake Whitefish and Cisco recruitment variability, respectively. These cross-lake analyses provided novel insights into important drivers of recruitment, the underlying mechanisms by which drivers act to regulate recruitment across environmental gradients, and how driver relative importance has changed through time in response to broad-scale climatic and ecosystem change. Collectively, this dissertation advanced understanding of the early life-history of these two species, how recruitment responded to past perturbations, and how populations may respond to future climatic and ecosystem change.