<p>Littoral-benthic habitats can play a key role in governing whole ecosystem production within lakes. Controls of littoral-benthic production can include light, nutrients, and grazers, although studies examining production across the photic zone in deep lakes are limited. This study investigates the role of nutrient limitation and inhibition from the shallow to deep (lower limit of the photic zone) littoral-benthic habitat of lakes with varying trophic states. We use a combination of nutrient-diffusing substrata (NDS), water column nutrient data, and photosynthetically active radiation (PAR) measurements. We observed that periphyton nutrient limitation and inhibition vary with depth and habitat. Differences were primarily driven by the concentration of dissolved inorganic nitrogen (DIN) and the availability of PAR. Less DIN and more PAR favored N limitation and P inhibition, whereas more DIN and less PAR favored P limitation and N inhibition. Furthermore, we found that differences in nutrient limitation in the shallow littoral-benthic habitat may be driven more by biological factors (e.g., predator density) than by variation in physical habitat heterogeneity. Our findings reveal that periphyton nutrient responses across the littoral-benthic zone for clear lakes are context-dependent. The shifting roles of nitrogen and phosphorus across depth gradients call for a more nuanced understanding of periphyton responses in lakes with extensive photic zones. Considering the importance of littoral-benthic habitat for whole lake function, additional studies exploring the role of nutrient, light, and consumers should occur across depth for clear, deep-water lakes.</p>