Recent observations have shown that increases in climate change-related coral mortality cause changes in shallow coral reef community structure through phase shifts to alternative taxa. As a result, sponges have emerged as a potential candidate taxon to become a “winner,” and therefore a numerically and functionally dominant member of many coral reef communities. But, in order for this to occur, there must be sufficient trophic resources to support larger populations of these active filter-feeding organisms. Globally, climate change is causing an increase in sea surface temperatures (SSTs) and a decrease in salinity, which can lead to an intensification in the stratification of shallow nearshore waters (0–200 m), that affects both the mixed layer depth (MLD) and the strength and duration of internal waves. Specifically, climate change-driven increases in SSTs for tropical waters are predicted to cause increased stratification, and more stabilized surface waters. This causes a shallowing of the MLD which prevents nutrients from reaching the euphotic zone, and is predicted to decrease net primary production (NPP) up to 20% by the end of the century. Lower NPP would subsequently affect multiple trophic levels, including shallow benthic filter-feeding communities, as the coupling between water column productivity and the benthos weakens. We argue here that sponge populations may actually be constrained, rather than promoted, by climate change due to decreases in their primary trophic resources, caused by bottom-up forcing, secondary to physical changes in the water column (i.e., stratification and changes in the MLD resulting in lower nutrients and NPP). As a result, we predict sponge-dominated tropical reefs will be rare, or short-lived, if they occur at all into the future in the Anthropocene.