Isolation of causative factors has proved challenging in characterizing the physical, chemical, and biological effects of shoreline hardening on the nearshore environment because of logistical challenges in identifying comparable sites. Extensive shoreline hardening and interspersion with unaltered shores in the large, shallow lakes in central Wisconsin provide an opportunity to surmount this. We compared the effects of shoreline protection on wave climate, bottom topography and substrate, water quality, and plant and animal assemblages at five adjacent pairs of natural and armored (riprapped) shorelines. Armored shorelines were characterized by coarser, more compacted substrates with lower organic content; cooler temperatures with higher dissolved oxygen; and greater water clarity. Differences in physical and chemical properties likely influenced plant growth forms and fish feeding guild differences between riprapped and natural sites. For example, floating-leaved plants were more abundant and fish were nearly twice as abundant and were represented by larger individuals at natural versus armored shorelines. Substrate characteristics may account for the differences in water quality and plant and animal associations observed in this study. As shoreline property owners continue to install riprap as protection against erosion, we expect the nearshore environment and associated biological communities to increasingly reflect this practice.