Individual-based models (IBMs) have been used to predict hydropower effects on fish populations since the 1990s. Designed to overcome the limitations of “habitat suitability” models, IBMs can make testable predictions of how alternative flow and temperature regimes affect populations. We have modeled instream flow and temperature effects on trout and salmon, effects of hydropower peaking on trout and juvenile pikeminnow (a desert species that uses backwaters as habitat), effects of salmon restoration flows on a frog that breeds in rivers, and flow effects on a warmwater herbivore. Lessons from this experience include: (1) Many hydropower management questions concern variation over time, so models need to include time; and there are many reasons to doubt that observed habitat “suitability” represents habitat quality. For these and other reasons, habitat models like PHABSIM are of questionable value. (2) When fish are assumed able to adapt their feeding site, moderate levels of within-day flow peaking is predicted to have minor if any effect. (3) The assumption that natural flow regimes protect native fish is valuable but should be applied cautiously in highly modified systems. (4) Temperature management for coldwater species often focusses on effects of summer peak temperatures, but populations can be affected as much by effects of temperature on growth in other seasons. (5) The primary concerns for protecting aquatic populations should always be providing food and feeding habitat and, often, protection from predation. Building IBMs requires time and expertise, and traditional validation is not always possible; however, the modeling process provides a valuable framework for organizing knowledge, clarifying and testing beliefs and mental models, and ensuring that field studies contribute to improved decision-making. Information on our models is at www.humboldt.edu/ecomodel.