Water exchange between streams and groundwater (hyporheic exchange) facilitates exchange of heat, nutrients, toxics, and biota. In-stream geomorphic structures (IGSs) such as log dams and steps are common in natural streams and stream restoration projects, and can significantly enhance hyporheic exchange. Hyporheic exchange is known to moderate temperatures in streams, a function important to a variety of stream organisms. Nevertheless, the connection between IGS form, hydrogeologic setting, hyporheic exchange, and hyporheic thermal impacts are poorly known. In this dissertation, I used hydraulic modeling and field experiments to quantify how basic characteristics of IGSs and their hydrogeologic setting impact induced hyporheic water and heat exchange and stream temperature. Model results indicate that structure size, background groundwater discharge, and sediment hydraulic conductivity are the most important factors controlling induced hyporheic exchange. Nonlinear relationships between many such driving factors and hyporheic exchange are important for understanding IGS functioning. Weir-induced hyporheic heat advection noticeably affected shallow sediment temperatures during the field experiments, and also caused slight cooling of the surface stream, an effect that increased with weir height. Nevertheless, such advection was far less important to the stream heat budget than atmospheric heat exchange, indicating streambed hydraulic conductivity was the overriding factor controlling hyporheic influence on surface water temperatures. Lotic organisms are adapted to the thermal regime typically experienced in their native ranges, and are therefore sensitive to thermal shifts from human activities. However, a basic survey of ecological sensitivity to temperature change in lotic systems is currently lacking. In this dissertation, I generated a quantitative synthesis of ecological sensitivity to temperature from the peer-reviewed scientific literature which I compared to a broad array of human thermal impacts to streams and rivers. Results indicate that on average, lotic organisms are more sensitive to warming than to cooling, and fish are more sensitive than invertebrates. Human thermal impacts entail warming more often than cooling and are of similar magnitude to that required to induce a 50% reduction in organism level functioning, indicating significant potential to impair ecological functioning. My results highlight the need for thermal mitigation in lotic systems at local, regional, and global scales.