The production of heterotrophic biomass is an important aspect of overall ecosystem functioning. However, single-celled organisms or microscopic metazoans are often ignored in studies of secondary production, despite being very abundant and possessing high mass-specific population growth rates, relative to the more widely studied larger taxa. Here, we focused on how life history parameters scale with body size of ciliates and meiofauna (body mass range from approximately 0.001 to 90 mg C/individual) and integrated experimental and survey data to calculate secondary production of these groups. First, we derived a single allometric scaling relationship between the intrinsic rate of population increase and body mass in a laboratory experiment. We then used this relationship to calculate secondary production for over 260 of these small species in the field, using survey data from two contrasting streams; one of which was nutrient rich, the other nutrient poor. Results from laboratory cultures showed that the scaling relationship between body mass and both daily intrinsic rate of population increase and generation time followed a power law. The relationship between body mass and annual secondary production was consistent in both streams, but the number of taxa was greater in the more productive site. Both ciliates and meiofauna had high rates of biomass production, with annual P/B ratios (production divided by biomass) for the whole assemblage exceeding 11 in both streams. We conclude that a large fraction of benthic production is overlooked when protozoans and microscopic metazoans are excluded from estimates of biomass turnover.