A laboratory flume was constructed to examine substrate effects on aquatic development. The flume was designed as a once-through system with a submerged cobble-filled corebox. Lake whitefish (Coregonus clupeaformis) embryos and temperature probes were deployed at multiple sites within the cobble and in the open water channel. Embryos were incubated in the flume for two different experimental periods: one to examine substrate impacts during natural lake cooling (37 days: 5 December 2016 to 10 January 2017) and the second to investigate substrate effects while administering a twice weekly 1 h heat shock (51 days: 11 January to 2 March 2017). During incubation, no significant difference was found in the average temperature between locations; however, temperatures were more stable within the cobble. Following both incubation periods, embryos retrieved from the cobble were significantly smaller in both dry mass and body length by up to 20%. These results demonstrate differences between embryos submerged in a cobble substrate and in the open water column, highlighting the need to consider the physical influences from the incubation environment when assessing development effects as part of any scientific study or environmental assessment. K E Y W O R D S cobble, embryonic development, lake whitefish, spawning ground substrate, temperature, thermal discharge 1 | INTRODUCTION Natural or anthropogenic changes in environmental conditions, in particular temperature, can have significant impacts on embryogenesis in aquatic poikilotherms. Within tolerance ranges for embryonic survival, these alterations can influence development rate, resulting in advanced or delayed hatching (Lim et al., 2017). Changes in hatch timing can subsequently impact survival in larval fish through trophic mismatch or by embryos hatching at a more or less developed phenotype (Cushing, 1990). Anthropogenic influences, such as cooling water discharges, are of particular concern to species that spawn in shallow water locations near industrial sites. Numerous studies have investigated the impacts of rearing temperature on embryonic development in salmonids with respect to hatching, size and other physiological parameters. In general, warmer temperatures will result in a shorter time to hatch (Sharpe and DeMichele, 1977). In lake whitefish (Coregonus clupeaformis), the time from fertilization to median hatch can range from 180 days down to 60 days, with embryos raised at a constant incubation temperatures