A long-term history of water table fluctuations, from alternating periods of drought and abundant precipitation, can be preserved in the stratigraphy of wetland sediments. We examined the middle to late Holocene history of vegetation and climate change from a small wetland on the Modoc Plateau in Shasta County, northeastern California. This site is at a transition between the Great Basin and the Californian Floristic Provinces, and the paleoecological record from Flycatcher Basin exhibits affinities to both. Although the sedimentary record extends back to ca. 8300 cal yr BP, organic sediment did not form until ca. 4500 cal yr BP, indicating that water was probably absent in the basin during the middle Holocene. Pollen and plant macrofossils deposited after 4500 cal yr BP suggests a mixed conifer – Quercus forest grew around Flycatcher Basin. Charcoal is abundant in these sediments, indicating periodic forest fire. Distinctly modern forests developed by about 2200 cal yr BP, when Pinus became the dominant conifer with Quercus, in a more closed forest, perhaps with more frequent fire. The record from Flycatcher Basin provides no evidence for change in the boundaries between the Great Basin and California (Cascadian) floristic provinces during the period of record. The late Holocene is interpreted as a generally increasingly mesic sequence, with a long-term increase in groundwater recharge, yet interspersed by extended drought during the last 2000 yr. Extended droughts occurred from ca. 1125 AD to 1450 AD, with an earlier protracted dry period from ca. 100 AD to ca. 900 AD. Generally wetter periods occur from ca. 1000 to 1125 AD, and after ca. 1450 AD. The paleoenvironmental changes in the Flycatcher Basin wetland are a local expression of a much broader climatic pattern, as shown by several studies of higher resolution proxies. The record from Flycatcher Basin wetland is important in demonstrating the centennial to millennial-scale fluctuations in water availability in a region of rapidly expanding human population, with an increasing need for water resources.