Larval sex dimorphism, fecundity, and sex ratios have been rarely studied in lotic insects, but can have ecological, energetic, and evolutionary importance. I evaluated the effect of microhabitat quality on larval and pupal sex dimorphism and sex ratios using a Hawaiian chironomid (Telmatogeton torrenticola Terry) and examined differences between sex-corrected and noncorrected biomass and secondary production estimates. Larvae and pupae were collected from two microhabitat types defined by microscale flow hydraulics to test for habitat effects on sex dimorphism, sex ratios, fecundity, standing stock biomass, secondary production, and Production/Biomass (P/B) ratios. Female larvae were more than twice as large as males, and this was more pronounced in pupae. Males were twice as abundant as females, and there was no effect of habitat on fourth-instar density. There was, however, a significant habitat effect on morphology, larval body size, standing stock biomass, secondary production, and P/B ratios. Biomass was not statistically different between sexes, but sex-corrected biomass was significantly lower than noncorrected biomass in both habitats but is likely not biologically significant. Sex-corrected secondary production estimates were 69–85% of noncorrected estimates depending on habitat, and sex correction did have a significant effect on P/B ratios in microhabitats of lower quality. This study is one of the first to address sex dimorphism and sex ratios in estimates of standing stock biomass and secondary production, providing initial evidence that microhabitat quality is important to understanding chironomid population biology and the potential role of sex-related demographics in estimates of productivity.