The temperatures of stream water and hyporheic water were monitored in spawning areas of an upland stream (Girnock Burn) and a degraded lowland stream (Newmills Burn). Both streams are located in North-east Scotland and are spawning streams for Atlantic salmon, Sabno salar L., and brown trout, S. trutta L. Monitoring between the spawning and hatching of ova revealed significant differences in the thermal regimes of the two sites. Whilst temperatures in stream and hyporheic water were similar in the Girnock, notable attenuation in the Newmills Burn resulted in increasing moderation of thermal regime with hyporheic depth. This probably reflects contrasting groundwater-surface water interactions in the two systems. In the Girnock an open gravel stream bed and lack of groundwater influence resulted in stream water downwelling through the gravel. In contrast, fine bed sediments and local groundwater inputs resulted in more complex stratification of temperatures in Newmills Burn. However, even in the conditions of the Newmills Burn, temperature based salmonid embryo development models predicted that egg burial depth has an insubstantial effect on ova development.