Incorporating organismal hydrogen (δ2H or δD) and oxygen (δ18O) stable isotope ratios into aquatic food web research can help elucidate relative reliance on shoreline inputs and/or feeding at different trophic levels; however, their interpretation is complicated by the fact that aquatic organisms derive hydrogen and oxygen from both their diet and the ambient water in which they reside. We examined spatial and seasonal patterns in δ2H and δ18O of field-collected water and small-bodied fishes. Samples were gathered from nearshore Lake Michigan, a dynamic region of a large, increasingly oligotrophic freshwater lake. We examined seasonal and spatial δ2H and δ18O values of surface and bottom water, and compared spatial δ2H and δ18O values of young-of-year yellow perch (Perca flavescens) and seasonal δ2H and δ18O values of round goby (Neogobius melanostomus). Nearshore δ2H and δ18O water values were more variable than previously-described offshore values. Variation in nearshore water δ2H and δ18O values was likely related to differential precipitation and/or discharges from tributaries, and there may be a surface dilution effect which led to lower δ18O values in nearshore surface waters than bottom waters. In our study, fish tissue δ2H and δ18O also varies more spatially than seasonally, and some findings suggest that fish tissue δ2H may reflect feeding at higher trophic levels. Though characteristics of the study system affect their interpretation, we suggest that δ2H and δ18O can be another tool to assess food web structure, with δ2H in particular having potential to resolve questions when δ13C or δ15N are inconclusive.