Global change will likely drive regional shifts in species distribution and localised changes in communities. In aquatic communities, altered drought regimes could be detrimental to the organisms that inhabit affected systems. Furthermore, stress-tolerant species are likely to be more susceptible to these changes, particularly if these species lack the capacity to disperse to new habitats. Kōwaro (Canterbury mudfish, Neochanna burrowsius) is a critically endangered stress-tolerant fish largely restricted to isolated populations in agricultural catchments scattered across the Canterbury Plains on South Island, New Zealand. Consequently, knowledge of how kōwaro respond to increased drying intensity and the likely mechanisms associated with these changes could considerably improve conservation efforts for this rare endemic fish. When exposed to two consecutive extreme droughts, a large network of kōwaro populations switched from adult-dominated populations to fry-dominated populations, which indicated a reduction in likely population resilience. Further investigation of kōwaro populations and associated trophic dynamics with stable isotopes along a drying gradient, indicated that drying-prone sites had higher relative abundance of kōwaro fry, which likely led to increased cannibalism by larger kōwaro. Importantly, increased canopy cover was associated with elevated abundance of terrestrial prey entering the aquatic system, with this food resource becoming increasingly important for larger kōwaro. Consequently, increased riparian planting could potentially offset the negative effects of increased drying by facilitating increased survival of larger kōwaro. Therefore, within degraded systems, additional environmental gradients, like the drying and canopy cover effects detected here, likely alter the trophic interactions and population dynamics of stress-tolerant species, providing both challenges and opportunities for their conservation.