We collected data for five years from the lower Missouri River including discharge (819–10032 m3s−1), mean depth (2.7–9.3 m), underwater irradiance (0.1–3.7 Ein m−2d−1), suspended solids (19–2340 mg L−1), total phosphorus (131–1810 μg L−1), total nitrogen (0.9–4.2 mg L−1), nitrate-N (380–3050 μg L−1), silica (8.2–16.8 mg L−1) and chlorophyll (4.5–107 μg L−1). Suspended solids, phosphorus and light attenuation varied directly with discharge. Nitrate, ammonium-N, silica and chlorophyll were strongly seasonal. Chlorophyll was temperature dependent exhibiting winter minima (<8 μg L−1) and spring and fall maxima (>40 μg L−1). In the growing season, chlorophyll co-varied with light and varied inversely with silica and dissolved P. Poor light conditions (mixed depth:photic depth > 10) and rapid flow rates (≈ 150 km d−1) suggest thatin situproduction of algae is less important than flux of biomass from upstream. Chlorophyll flux and pheophytin increased with discharge indicating contributions of benthic or terrestrial inputs. About a fourth of the particulate organic nitrogen transported by the river may be autochthonous. Algal uptake may reduce silica flux by >22%.