We determined the spatial and temporal distribution of major plant nutrients, dissolved oxygen, chlorophyll-a and primary production, at three deep-water locations in Lake Tanganyika to infer patterns of water displacements and to interpret the impact of wind-generated changes in nutrients on the timing and magnitude of phytoplankton production.

In the southern end of the lake, the onset of cooler, windier conditions during May–September caused stratification weakening, tilting of isotherms and upwelling of dissolved inorganic nitrogen and soluble reactive phosphorus from nutrient-rich deeper waters. These factors coincided with an increase in chlorophyll-a concentrations but not with clear evidence of increased primary production. An internal seiche at that time seemed associated with similar but less pronounced events at the other stations after cessation of the winds.

We suggest that internal seiching can spread kinetic energy throughout the lake, triggering upward nutrient fluxes through mixing elsewhere. The response to water displacements in terms of nutrient supply to the epilimnion seems to be governed by differences in the strength of vertical temperature, and by nutrient and dissolved oxygen gradients. At the most northern station, these gradients were strongest and closest to each other and throughout the year primary production rates, phosphorus and chlorophyll-a concentrations in the euphotic zone appeared generally higher than at the other stations, probably also because of increased nutrient input from the Rusizi River.

We emphasise that the intra- and interannual differences between the strength of lake stratification and wind regime are of major importance in determining the extent of upwelling events upwind as well as internal seiching strength and duration. That consequently affects the extent of internal nutrient loading throughout the lake and ultimately plays an important role in the lake trophic status.

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