Humans preferentially settle near freshwaters, including along the shorelines of lakes. Associated with this human behavior are changes to riparian and littoral habitats of lakes that likely have serious consequences for aquatic food webs. Because of the tight coupling between riparian and aquatic habitats, I hypothesized that this human disturbance would alter terrestrial-aquatic linkages on lakes, impacting trophic interactions and ecosystem function. In a survey of 25 lowland Pacific Northwest lakes, along a gradient of shoreline development, I found that the density of riparian trees and woody debris, and the organic content of littoral sediments, declined significantly with shoreline development. My results demonstrate that coarse wood is a physical structure that retains organic matter in shallow waters where it is available for biotic processing. I quantified the effects of riparian deforestation on terrestrial insect subsidies to fish and found that terrestrial insects comprised up to 100% of fish diets in two lakes with intact riparian vegetation, versus a maximum of 2% of fish diets in two urban lakes, results confirmed by a sampling survey of 28 Pacific Northwest lakes and a literature review of 25 North American lakes. I also found that fish in undeveloped lakes daily consume up to 3x the amount of energy consumed by fish in urban lakes. I further investigated the role of shoreline development in reducing terrestrial subsidies to zooplankton using carbon stable isotopes from 28 lakes of varying shoreline development intensity. Carbon isotope data of zooplankton and surface particulate organic matter did not reflect variation in terrestrial support of zooplankton with shoreline development, but rather the vertical distribution of primary production in lakes. Shoreline development affected the distribution of phytoplankton by altering the spatial segregation of surface and subsurface layers of production. Finally, I investigated the use of science in local habitat protection regulations, and found that incorporation of scientific information into land-use planning rules is not uniform across all jurisdictions, but that the use of peer-reviewed literature varies by jurisdiction size and resource base. My results highlight the importance of aquatic-terrestrial linkages for lake habitat structure and food web interactions.