Regulated rivers are typically managed for a variety of water users, resulting in flow regimes that differ from natural ones that shaped the resident biotic community.  Impacts from water regulation on benthic macroinvertebrate (BMI) and river breeding amphibians remains poorly studied. We summarize here three studies on foothill yellow-legged frog (Rana boylii) and BMI characteristics associated with water management, including recreational boating flows, on the regulated North Fork Feather River from 2002-2007.  Our initial study focused on evaluating direct impacts of recreational flows on frogs and BMI via pre and post flow counts.  Subsequent studies utilized a BACI design to compare frog population and BMI community characteristics in two reaches, one of which was exposed to summer boating flows.  BACI results showed that pulse flows (or the new license flow regime) during the late summer were associated with a declining adult frog population.  BMI drift increased sharply during pulsed-flow events and community measures tended to decline.  These studies illustrate important mechanisms for biological impacts from regulated flows that do not conform to the natural flow regime.