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Abstract: The reconstruction of paleoenvironmental changes from diatoms in lake sediments is based on the usual assumption that, in each studied sample, the dominant species reflect the environment that prevailed during the time of deposition. If the environment changed significantly during the period of deposition (several years) one can expect a mixture of species having different or contradictory ecological affinities. In this paper we present analyses of diatoms in surface sediment samples collected in the Lake Ossa area (3°50′N, 9°36E) and fossil diatoms from a mid-late Holocene core retrieved in the deepest part of the lake. The Lake Ossa area alternates between a short dry season centered at around the northern winter and a long rainy season during the rest of the year entailing significant changes in water level and pH. Based on multivariate analyses, we will show here that mean annual water depth is the most significant variable explaining the distribution of diatoms in the entire Lake. However, seasonal changes of water level are poorly recorded by diatom assemblages, except in some flat areas on the borders of the lakes where a mixing between species with different affinities to water depth is likely due to seasonal changes in water level. Inferred water depth based on a quantitative transfer function reflected essentially secular to millennial changes in the studied core. The relationship between pH and diatoms is not statistically significant but seasonal to multi-annual pH variations mainly observed in the central parts of the lake are reflected by a mixing of acidophilous and alkaliphilous species. Hierarchical ascending cluster analysis (HAC) considered as the most efficient mean of describing diatom mixing shows that seasonal to multi-annual changes in pH are recorded both in the modern and fossil assemblages. According to the degree of mixing between diatoms with different pH affinities we conclude that short-term pH variability was weaker than today between 5200 and 2700calyrBP, stronger between 2700 and 2000calyrBP, weaker again between 2000 and 600calyrBP and similar to present from 400calyrBP onwards. Short-term changes were thus superimposed on secular to millennium trends recorded by modifications in the abundance of alkaliphilous diatoms. All these changes are interpreted as variations in precipitation according to a previous model showing that pH is strongly controlled by acidic meteoric water. Inferred water depth slightly changed over the last 5500years showing weak variations of precipitation minus evaporation balance at secular to millennial time scales. These results will be used to refine previously published paleoclimatic interpretations, which explained changes in precipitation and P–E balance by modifications in the vertical structure of the atmosphere and subsequently by changes in cloud cover, convective or stratiform. [Copyright &y& Elsevier]