Diatom genera in many large East African lakes change little throughout the Holocene period suggesting relatively stable ecological conditions and some resilience to environmental change. Ecosystem stability is less common in smaller, more sensitive lakes, such as those within volcanic craters, where external impacts can cause abrupt and rapid fluctuations. A 4100-year diatom and cyanobacteria pigment record from Lake Massoko, a volcanic crater lake in southern Tanzania, is used to illustrate important switches in resource ratios following tephra deposition 1190 years ago. It is hypothesized that the tephra reduced the rate of P diffusion from the sediments and increased the Si:P ratio in the lake. A period of acute change in planktonic diatom communities resulted from the tephra impact and lasted c. 110 years. The magnitude of the change shown by the diatoms and their slow recovery from the tephra may be due in part to a coincident fall in lake level caused by a reduction in regional rainfall. The statistical significance of the tephra impact relative to that of catchment and climate change has been tested using variance partitioning and rate-of-change analysis. Multiproxy indicators show an important period of positive water balance 1700 ago and a relatively dry episode persisting between 1000 and 400 years ago. The lake ecosystem is shown to be highly sensitive to both climate change and tephra deposition.