Excess phosphorus inputs to streams can lead to eutrophication, degraded water quality, and decreased biodiversity. Stream ecologists have found only weak relationships between dissolved reactive phosphorus (DRP) and epilithic biomass. If sediment bound phosphorus correlates with soft sediment primary production, then soft sediment periphyton maybe a better indicator of eutrophication in streams. However, algal dynamics on soft sediments are rarely studied. We examined differences in primary production and chlorophyll a on hard and soft substrata in seven agricultural headwater streams in central Illinois. Net primary production was estimated using the light–dark oxygen method in replicate acrylic chambers (20x7 cm) with sediments or artificial hard substrata during the summers of 2005 and 2006. Chlorophyll a was significantly higher on soft versus hard substrata except for two streams in August 2006. Net primary production on soft sediment was higher than on hard substrata and appears to be better correlated with sediment bound phosphorus than DRP. These methods suggest that periphyton on soft sediments are an important contributor to whole system primary production in streams. Soft sediments, therefore, maybe a driving force in the diurnal dissolved oxygen fluctuations and water quality in these sand/gravel dominated streams.