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Differences among lake morphologies often explain variation in characteristics of lentic ecosystems. Although beaver ponds also vary in morphology, previous studies have not examined the effects of such variation on downstream ecosystems. This study evaluated downstream effects of multiple beaver ponds in the Colorado Rocky Mountains during one low and one high-flow year. Beaver pond morphology was described as the natural log transformed ratio of beaver dam height (which determines hydraulic head) to pond surface area and related to pond spillover phytoplankton and characteristics of the ecosystem downstream (nutrient concentrations, limiting nutrients, periphyton, benthic organic matter (BOM), and benthic invertebrate consumers). Nitrate concentration increased systematically downstream of beaver ponds, but only in the low flow year when groundwater influences predominated. Effects of beaver ponds on soluble reactive phosphorus concentration depended on pond morphology, increasing downstream of small ponds with high dams, but only during the low-flow year. In situ experiments showed that neither beaver activity nor pond morphology predicted periphyton-limiting nutrients downstream. Both periphyton biomass and BOM decreased downstream of small ponds with high dams but pond morphology did not predict abundance of invertebrate grazers or detritus-feeding consumers. While suspension feeding invertebrates increased downstream from small ponds with high dams, variation in chlorophyll a from water spilling over beaver dams did not follow a similar pattern. We conclude that the effects of beaver ponds on downstream nutrients, resources and consumers are rarely systematic, but instead depend on variation in pond morphology and on annual hydrologic variation.