AbstractGroundwater–surface water (GW–SW) interactions represent an important, but less visible, linkage in lake ecosystems. Periphyton is most abundant at the GW–SW interface and can rapidly assimilate nutrients from the water column. Despite the importance of periphyton in regulating whole‐lake metabolism, they are less well studied or monitored in comparison with planktonic taxa and pelagic systems. This is in stark contrast to studies of flowing waters and wetlands, where variability in GW–SW connectivity and periphyton productivity is more often incorporated into study designs. To bridge the gap between groundwater's influence on lake benthic communities, this synthesis aims to prime researchers with information necessary to incorporate groundwater and periphyton sampling into lake studies and equip investigators with tools that will facilitate cross‐disciplinary collaboration. Specifically, we (1) propose how to overcome barriers associated with studying littoral ecological‐hydrological dynamics; (2) summarize field, laboratory, and modeling techniques for assessing spatiotemporal periphyton patterns and benthic hydrological fluxes; and (3) identify paths for hydrological techniques to be incorporated into ecological studies, deepening our understanding of whole‐lake ecosystem function. We argue that coupling hydrological and periphyton measurements can yield dualistic insights into lake ecosystem functioning: how benthic periphyton modulate constituents within groundwater, and conversely, the extent to which constituents in groundwater modulate the productivity of periphyton assemblages. We assert that priming ecologists and hydrologists alike with a shared understanding of how each discipline studies the nearshore zone presents a tangible path forward for both integrating these disciplines and further contextualizing lake processes within the limnological landscape.