Animals with resource-based breeding systems show varying sexual selection modes driven by resource availability. Males of the freshwater goby Tridentiger brevispinis (Pisces: Gobiidae), which are larger, with a longer dorsal-fin, than females, make nests under stones, and provide exclusive parental care of eggs in the nests. For this goby, the nest sites are crucial resources for reproduction. Laboratory experiments that controlled for nest-site abundance were conducted to investigate the effects of nest-site availability on male-male competition and female mate choice. Nest-holding males were on average larger than the average size of all males combined under conditions of low nest-site availability. This result indicates a greater advantage for large males in intrasexual competition for nest sites under conditions of low nest-site availability. Furthermore, egg-guarding males under conditions of low nest-site availability were larger than nest-holding males without eggs. Under conditions of high nest-site availability, the dorsal-fin length of nest-holding males with eggs were longer than those without eggs. These findings suggest that female preference for mates varies qualitatively with nest-site availability. This variation in female preference might result from mate availability that depends upon nest-site availability. The current study concludes that in nest-spawning fishes, nest-site availability can affect the intensity of male-male competition and cause variations of female preference for mates.