Abstract Global assessments evaluating greenhouse gas emissions and climate benefits of hydropower rely on life cycle assessments (LCAs). However, small hydropower plants (i.e. installations with less than 10 MW; SHPs), are largely underrepresented in such schemes, despite their widespread proliferation and well-known ecological concerns. Here we quantified, partitioned, and compared the net carbon (C) footprint of four temperate SHPs with different operation designs over a 100 year time horizon. In contrast with previous hydropower LCAs studies, we followed an integrative net C footprint approach accounting for all potential sources and sinks of C within the life cycle of the studied SHPs, including both biogenic and non-biogenic sources, as well as for the pre- and post-impoundment stages involved in the flooding of the reservoir. We found that the areal and system-level C emissions were mostly driven by the residence time of the impounded water, which in turn was linked to the SHP operation type. The power installed in the SHPs did not have a relevant role on the net C fluxes. Accordingly, SHPs with smaller water storage capacity were almost neutral in terms of the C footprint. In contrast, SHPs with water storage facilities prolonged the water residence time in the reservoir and either acted as a source or sink of C. The long water residence time in these SHPs promoted either emission of biogenic gases from the surface or C storage in the sediments. Our work shows that integrative net C footprint assessments accounting for different operation designs are necessary to improve our understanding of the environmental effects of SHPs.