In the Australian wet–dry tropics, seasonal changes in hydrology can influence abiotic conditions and consequently influence standing stocks of benthic biomass and production. While there is some understanding of these processes at riverscape scales, effects of seasonal hydrology on benthic biomass and production in low-order streams remain largely unquantified. We observed changes in water quality, algal and macroinvertebrate biomass, and stream benthic primary productivity over a 15-month period in three low-order streams with contrasting flow regimes in the wet–dry tropics of northern Australia. Water quantity and quality showed a distinct seasonal signature reflected in seasonal peaks in algal (maximum 1.29 µg cm−2) and macroinvertebrate biomass (maximum 0.24 g m−2), and productivity (maximum 0.41 g C m−2 days−1). In particular, transitional periods between dry and wet seasons were key times of elevated production and algal biomass. Overall, variation in biomass and benthic primary production was greater between seasons than among streams indicating that extrapolation between seasons may not be appropriate.