Anthropogenic impacts, including urbanization, deforestation, farming, and livestock grazing have altered riparian margins worldwide. One effect of changes to riparian vegetation is that the ground-level light, temperature, and humidity environment has also been altered. Galaxias maculatus, one of the most widely distributed fishes of the southern hemisphere, lays eggs almost exclusively beneath riparian vegetation in tidally influenced reaches of rivers. We hypothesized that the survival of these eggs is greatly affected by the micro-environment afforded by vegetation, particularly relating to temperature, humidity and UVB radiation. We experimentally reduced riparian vegetation height and altered shading characteristics, tracked egg survival, and used small ground-level temperature, humidity and UVB sensors to relate survival to ground-level effects around egg masses. The ground-level physical environment was markedly different from the surrounding ambient conditions. Tall dense riparian vegetation modified ambient conditions to produce a buffered temperature regime with constant high relative humidity, generally above 90%, and negligible UVB radiation at ground-level. Where vegetation height was reduced, frequent high temperatures, low humidity, and high UVB irradiances reduced egg survival by up to 95%. Temperature effects on egg survival were probably indirect, through reduced humidity, because developing eggs are known to survive in a wide range of temperatures. In this study, it was remarkable how such small variations in relatively small sites could have such a large effect on egg survival. It appears that modifications to riparian vegetation and the associated changes in the physical conditions of egg laying sites are major mechanisms affecting egg survival. The impacts associated with vegetational changes through human-induced disturbances are complex yet potentially devastating. These effects are particularly important because they affect a very small portion of habitat that is required to complete the life history of a species, despite the wide distribution of adults and juveniles across aquatic and marine environments.