Survival rate of the larval stage is an important driver of fish recruitment. To understand mechanisms regulating larval survival it is important to understand the relative importance of abiotic and biotic factors that shape larval spatial distributions. We studied larval Coregonus distributions in surface waters (surface to 1 m) by repeatedly sampling study sites in two lakes that varied greatly in trophic state and regional climate. We evaluated the importance of bathymetric depth, Julian Day, edible zooplankton densities (EZ, ind. L⁻¹) and wind vectors on larval spatial distributions using generalized additive modeling. In both systems, larval counts declined in a negative exponential fashion with bathymetric depth, indicating shallow depths are critical nursery habitat. The north-south wind vectors and Julian Day (which was positively correlated with surface temperature) influenced larval distributions in Lake Geneva with larval counts related to both variables linearly, whereas the east-west wind vector and EZ were unimportant. Highest larval counts were during an offshore south wind and declined slightly with Julian Day. In Lake Superior, bathymetric depth and the east-west wind vector influenced larval distributions and were unrelated to EZ, Julian Day, and the north-south wind vector. Larval counts were highest when onshore southwest winds preceded sampling. Differences in how wind affected larval distribution (offshore vs. onshore) might be related to larval size with Lake Superior larvae considerably smaller (average length 12.9 mm vs. 15.9 mm); thus, more apt to be subjected to advection. Within coastal waters, Julian Day and wind vectors influence distributions, but their importance seemingly varies lake-to-lake.