Thermal structure, light attenuation, and chlorophyll- a dynamics within the upper 100 m at the northern and southern ends of Lake Tanganyika were measured from August 1995-July 1996. Pronounced variability of thermal structure in time, depth and region were observed. During the dry windy season (June-September), the water column in the south was largely isothermal down to 100 m, while in the north stratification was detectable. Subsequently, in October, cessation of winds coincided with a reestablishment and strengthening of thermal stratification in the south, and a distinct rise of a weakened thermocline in the north was accompanied by an increase in epilimnetic concentrations of dissolved solids. The depth of photic zone was highly variable with the average position of 1% of incident photosynthetically active radiance found between 20 and 70 m, sometimes showing vertical shifts of 25 m a week. Weekly observations showed that concentrations of chlorophyll- a were rather similar at both ends of the lake. At both stations, periods of unstable or absent thermal stratification were accompanied by increased concentrations of chlorophyll- a , although in the north chlorophyll- a also peaked during periods of deep thermal stratification and low rates of mixing. Concentrations of chlorophyll- a did not show significant relationship with the available amount of underwater available photosynthetically active radiance (I m from 11-173 w Em -2 s -1 ). We suggest that in Lake Tanganyika chlorophyll- a maxima can occur whenever growth rates exceed spatial mixing rates, that is, if mixing is less than a critical turbulence. Our observations underscore the consequences of hydrodynamic processes on biological productivity either by securing internal nutrients or by controlling the timing and magnitude of phytoplankton biomass production.