Galaxias gollumoides McDowall and Chadderton occurs in contrasting hydrological environments across Southland and Stewart Island, New Zealand. Our study experimentally investigated intraspecific variation in G. gollumoides from wetland and stream habitats, testing for phenotypic divergence in spawning substrate choice, and that spawning timing is influenced by the proximate hydrological and meteorological environments. Wetland and stream G. gollumoides displayed intraspecific behavioural divergence, utilising contrasting spawning substrates across multiple tanks, even when held in common experimental conditions. Galaxias gollumoides displayed intraspecific spawning timing differences with wetland‐sourced G. gollumoides spawning earlier than stream‐sourced G. gollumoides. Spawning also occurred significantly more often during peaks of warmer mean daily water temperature and barometric pressure, than during colder temperature, low‐pressure periods. Interannual variation in initial spawning timing was also attributed to differences in water temperature. In combination, experimental evidence‐ and field‐based observations support our hypothesis that G. gollumoides can utilise available substrates in habitats of contrasting hydrology and structure, while spawning timing is controlled by changes in proximate environmental conditions. These characteristics may enhance a population's recruitment success and the species persistence in the fluctuating hydrological environments of ephemeral wetlands and tributary streams that were once likely widespread in Southland.