Culvert replacements are commonly undertaken to restore aquatic organism passage and stream hydrologic and geomorphic conditions, but their effects on ecosystem processes are rarely quantified. The objective of this study was to investigate the effects of two culvert replacement designs on stream ecosystem processes. The stream simulation design, where culverts accommodate bankfull width and streambeds are reconstructed through the culvert, was compared with the bankfull and backwater design, where streambeds were left to fill naturally, as well as to non‐replaced culverts. We predicted that stream simulation culverts would best preserve water velocity and coarse particulate organic matter (CPOM) retention within the culvert relative to upstream reaches, and that both replaced culvert styles would exhibit rates closer to upstream reaches than non‐replaced culverts. In addition, we predicted that ecosystem processes (CPOM retention, transient storage and nutrient uptake) would be similar in reaches upstream and downstream of both replaced culvert styles, because both designs are constructed to maintain stream slopes and bankfull widths through the structure. We found that stream simulation design better maintained CPOM retention through culverts compared with non‐replaced and bankfull and backwater design culverts, but observed no differences in ecosystem processes between reaches located upstream or downstream of replaced culverts. Although the stream simulation design requires additional streambed construction relative to the bankfull and backwater design, this step may lead to additional improvement if maintaining ecological conditions through the culvert is an important restoration goal. Copyright © 2017 John Wiley & Sons, Ltd.