The current effort focuses on characterizing physical and biological conditions across the northwest Florida shelf during summer as they influence Karenia brevis distributions and phytoplankton/microphytobenthos community associations. Phytoplankton and benthic algal communities were examined in the context of cross-shelf hydrography and sediment conditions during July 2009 between the 20 and 65m isobaths off Panama City, FL. A towed undulating profiler (SeaSciences Acrobat) mapped water column characteristics between near-surface and ∼1m above the sediment. A CTD/rosette provided hydrographic profiles and collected water samples at 17 cross-shelf locations at selected depths for nutrient concentration, phytoplankton biomass determination, and chemotaxonomic and taxonomic phytoplankton identification. In addition, a CTD/rosette time series sample set was collected following a holey sock drogue set at ∼34m along the ∼50m isobath, and cores were collected at eight stations approximately along the 30, 40 and 55m isobaths. Cross-shelf, a pycnocline existed at ∼10m depth, the 1% light level penetrated to ∼45m depth, and nitrate–nitrite (NO3−+NO2−) concentrations increased in the lower 10m of the water column to the 50m isobath and then below 40-m depth to the 65m isobath. A chlorophyll a peak occurred near-bottom between the 25 and 35m isobaths. Gyroxanthin dinoflagellates (GD) representing K. brevis occurred across the shelf in near-surface and near-bottom waters. Near-surface GD co-occurred with cyanophytes at low density in the upper 20m of the water column where NO3−+NO2− concentrations were low. Above sediments in the euphotic zone, near-bottom GD were most abundant between the 25 and 35m isobaths where the NO3−+NO2− concentrations were 1–4µM and where microphytobenthos competed for nutrient sources. Below the euphotic zone, GD were present near-bottom to the 60m isobath where NO3−+NO2− concentrations approached 6µM. A pattern consistent with dinoflagellate diel vertical migration was inferred at the 50-m isobath time-series station. The results provide insight into offshore K. brevis seed populations and their associations with other phytoplankton and microphytobenthos. Under summer light and nutrient conditions along the northwest Florida shelf, K. brevis coastal blooms may be seeded by diffuse near-surface populations during occasional downwelling conditions and by more concentrated near-bottom populations during more prevalent upwelling conditions.