Three collecting trips were coordinated in April, May, and August 2006 to sample the water column and benthos of hypereutrophic Upper Klamath Lake (OR, USA) through the annual cyanophyte bloom of Aphanizomenon flos‐aquae. A pore‐water profiler was designed and fabricated to obtain the first high‐resolution (centimeter‐scale) estimates of the vertical concentration gradients of macro‐ and micronutrients for diffusive‐flux determinations. A consistently positive benthic flux for soluble reactive phosphorus (SRP) was observed with solute release from the sediment, ranging between 0.4 and 6.1 mg/m²/d. The mass flux over an approximate 200‐km² lake area was comparable in magnitude to riverine inputs. An additional concern related to fish toxicity was identified when dissolved ammonium also displayed consistently positive benthic fluxes of 4 to 134 mg/m²/d, again comparable to riverine inputs. Although phosphorus was a logical initial choice by water quality managers for the limiting nutrient when nitrogen‐fixing cyanophytes dominate, initial trace‐element results from the lake and major inflowing tributaries suggested that the role of iron limitation on primary productivity should be investigated. Dissolved iron became depleted in the lake water column during the course of the algal bloom, while dissolved ammonium and SRP increased. Elevated macroinvertebrate densities, at least of the order of 10⁴individuals/m², suggested that the diffusive‐flux estimates may be significantly enhanced by bioturbation. In addition, heat‐flux modeling indicated that groundwater advection of nutrients could also significantly contribute to internal nutrient loading. Accurate environmental assessments of lentic systems and reasonable expectations for point‐source management require quantitative consideration of internal solute sources.