Intertidal pools, created largely by stingray foraging over unvegetated sediment shores in Quandamooka provide important nursery habitats for the juveniles of commercially important whiting and prawns. Minjerribah (Stradbroke Island) locals report that sandy shores around Quandamooka are darkening in colour and suggested that this is due to increases in flood-derived mud deposits. While stingray foraging provides nursery opportunities for juvenile nekton their extensive and persistent bioturbation might rapidly incorporate settled, darker fine sediments decreasing sediment albedo and increasing absorption of solar radiation. This interaction might drive pool temperatures to the thermal limits of the pool dwelling nekton and their prey. To assess whether the thermal profiles of intertidal pools and sediments are affected by differences in sediment albedo, we used data loggers to measure temperatures of naturally occurring pools in sandy mud and muddy sand. Lower albedo sediments reached significantly higher temperatures than nearby higher albedo sediments (p < 0.001). Therefore, flood deposited muds could combine with atmospheric temperatures elevated by global warming to threaten intertidal species, particularly on low energy shores. The putative link between flood runoff and major Queensland fisheries provides a powerful lever with which to increase the intensity and scope for catchment-based solutions to sediment runoff.